Markers of Triple-Negative Breast Cancer And Uses Thereof

ABSTRACT

In one aspect provided herein are methods of determining a triple negative breast cancer (TNBC) subtype in an individual in need thereof comprising determining expression of one or more genes in one or more TNBC cells of the individual; and comparing the expression of the one or more genes in the TNBC cells with the expression of the one or more genes in a control. In another aspect, the methods are directed to methods of determining a treatment protocol for the TNBC patient based on the TNBC subtype. In another aspect, the methods are directed to predicting whether an individual will benefit from a treatment for a particular TNBC subtype. In yet another aspect, the invention is directed to a method of determining whether an agent can be used to treat a TNBC subtype.

RELATED APPLICATION

This application claims the benefit of U.S. Provisional Application No. 61/561,743, filed on Nov. 18, 2011.

The entire teachings of the above application are incorporated herein by reference.

GOVERNMENT SUPPORT

This invention was made with government support under grants CA95131, CA148375; CA105436 and CA070856, CA68485 and CA009385 awarded by the National Institute of Health (NIH). The government has certain rights in the invention.

BACKGROUND OF THE INVENTION

Treatment of patients with triple-negative breast cancer (TNBC), lacking estrogen receptor (ER) and progesterone receptor (PR) expression as well as human epidermal growth factor receptor 2 (HER2) amplification, has been challenging due to the heterogeneity of the disease and the absence of well-defined molecular targets (Pegram M D, et al. J Clin Oncol. 1998; 16(8):2659-2671; Wiggans R G, et al. Cancer Chemother Pharmacol. 1979; 3(1):45-48; Carey L A, et al. Clin Cancer Res. 2007; 13(8):2329-2334). TNBCs constitute 10%-20% of all breast cancers, more frequently affect younger patients, and are more prevalent in African-American women (Morris G J, et al. Cancer. 2007; 110(4):876-884). TNBC tumors are generally larger in size, are of higher grade, have lymph node involvement at diagnosis, and are biologically more aggressive (Haffty B G, et al. J Clin Oncol. 2006; 24(36):5652-5657). Despite having higher rates of clinical response to presurgical (neoadjuvant) chemotherapy, TNBC patients have a higher rate of distant recurrence and a poorer prognosis than women with other breast cancer subtypes (Haffty B G, et al. J Clin Oncol. 2006; 24(36):5652-5657; Dent R, et al. Clin Cancer Res. 2007; 13(15 pt 1):4429-4434). Less than 30% of women with metastatic TNBC survive 5 years, and almost all die of their disease despite adjuvant chemotherapy, which is the mainstay of treatment (Dent R, et al. Clin Cancer Res. 2007; 13(15 pt 1):4429-4434).

One of the first molecular insights into TNBCs was the observation that they are likely to arise in BRCA1 mutation carriers and have gene expression (GE) profiles similar to those of BRCA1-deficient tumors (Haffty B G, et al. J Clin Oncol. 2006; 24(36):5652-5657). BRCA1 plays an important role in DNA double-strand break repair, contributing to the maintenance of DNA stability (D'Andrea A D, Grompe M. Nat Rev Cancer. 2003; 3(1):23-34). Poly ADP-ribose polymerase (PARP) enzymes are critical for appropriate processing and repair of DNA breaks (Hoeijmakers J H. Nature. 2001; 411(6835):366-374). Tumor cell lines lacking functional BRCA1 or BRCA2 are sensitive to PARP inhibitors in preclinical studies (Farmer H, et al. Nature. 2005; 434(7035):917-921). Clinical trials using both PARP inhibitors and DNA-damaging agents (e.g., cisplatin) in TNBC are currently underway and show promise in BRCA1/2-mutant tumors (Fong P C, et al. N Engl J. Med. 2009; 361(2):123-134). Other studies identifying molecular markers of TNBC, such as VEGF (Burstein H J, et al. J Clin Oncol. 2008; 26(11):1810-1816), EGFR (Nielsen T O, et al. Clin Cancer Res. 2004; 10(16):5367-5374), Src (Finn R S, et al. Breast Cancer Res Treat. 2007; 105(3):319-326), and mTOR (Ellard S L, et al. J Clin Oncol. 2009; 27(27):4536-4541) have been important for the design of clinical trials investigating targeted treatments.

Clearly, there is a major need to better understand the molecular basis of TNBC and to develop effective treatments for this aggressive type of breast cancer.

SUMMARY OF THE INVENTION

In one aspect provided herein are methods of determining a triple negative breast cancer (TNBC) subtype in an individual in need thereof comprising determining expression of one or more genes (e.g., presence of one or more mRNAs proliferation genes, DNA damage response genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC BL1 subtype. Increased expression of one or more growth factor signaling genes, glycolysis genes, gluconeogenesis genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC BL2 subtype. Increased expression of one or more immune cell signaling genes, cytokine signaling genes, antigen processing and presentation genes, core immune signal transduction genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC IM subtype. Increased expression of one or more cell motility genes, extracellular matrix (ECM) receptor interaction genes, cell differentiation genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC M subtype. Increased expression of one or more cell motility genes, cellular differentiation genes, growth pathway genes, growth factor signaling genes, angiogenesis genes, immune signaling genes, stem cell genes, HOX genes, mesenchymal stem cell-specific marker genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC MSL subtype. Increased expression of one or more hormone regulated genes in the TNBC cells compared to the control indicates that the TNBC is a TNBC LAR type.

In another aspect, the methods are directed to methods of determining a treatment protocol for the triple negative breast cancer (TNBC) patient based on the TNBC subtype.

In another aspect, the methods are directed to predicting whether an individual (e.g., patient) will benefit from a (one or more) treatment for a particular TNBC subtype.

In yet another aspect, the invention is directed to a method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) subtype comprising contacting a cell line that is a model for the TNBC subtype of interest with an agent to be assessed; and determining viability of the cell line in the presence of the agent, wherein if the viability of the cell line decreases in the presence of the agent, then the agent can be used to treat the TNBC subtype of interest. The TNBC subtype of interest can be a TNBC BL-1 subtype, a TNBC BL-2 subtype, a TNBC IM subtype, a TNBC M subtype, a TNBC MSL subtype or a TNBC LAR subtype.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1C: Filtering GE data sets to identify TNBCs. (1A) Flow chart of analysis. Human breast cancer GE profiles (training=2353, validation=894) were normalized within individual data sets and a bimodal filter was applied to select ER, PR, and HER2 negative samples by GE, resulting in 386 samples in the training set and 201 samples in the validation set with a triple-negative phenotype. k-means clustering was performed on the training set, and a GE signature representing the TNBC subtypes from the training set was used to predict the best-fit subtype for each TNBC profile in an independent validation set. GSE-A was performed on the training and validation sets to identify enriched canonical pathways for each TNBC subtype. (1B) Histograms show the distribution and frequency of tumors using relative ER, PR, and HER2GE levels (log2) and bimodal fit to identify TN tumor samples. Dashed line indicates the expression value at the center of the positive expression peak used to select controls for C. (1C) Heat map representation of GE for 386 TNBCs relative to 5 IHC-validated controls for each ER, PR, and HER2.

FIGS. 2A-2E: Identification of TNBC subtypes. (2A) Silhouette plot showing the composition (n=number of tumors) and stability (AVG width) of k-means clustering on the TNBC training set. Clusters with s(I)>0 were considered stable. (2B) Consensus clustering displaying the robustness of sample classification using multiple iterations (×1000) of k-means clustering. (2C) The CDF depicting the cumulative distribution from consensus matrices at a given cluster number (k). (2D) The optimal cluster number is 7 at the point in which the relative change in area (A) under the CDF plot does not change with increasing k. (2E) Principal component analysis graphically depicting fundamental differences in GE between the TNBC clusters. The cluster (subtypes) are named as shown.

FIG. 3: GE patterns within TNBC subtypes are reproducible. Heat maps showing the relative GE (log2, −3 to 3) of the top differentially expressed genes (P<0.05) in each subtype in the training set (left) and the same differentially expressed genes used to predict the best-fit TNBC subtype of the validation set (right). Overlapping gene ontology (GO) terms for top canonical pathways in both the training and validation sets as determined by GSE-A are shown to the right of the heat maps.

FIGS. 4A-4F: Basal-like TNBC subtypes have differential sensitivity to DNA-damaging agents. IC50 values for TNBC cell lines treated with PARP inhibitors (4A) veliparib, (4C) olaparib, or (4E) cisplatin for 72 hours. Error bars reflect SEM for 3 independent experiments. Black horizontal lines above various bars in the plots indicate cell lines that failed to achieve an IC50 at the highest dose of veliparib (30 μM), olaparib (100 μM), or cisplatin (30 μM). Cell lines that carry BRCA1 or BRCA2 mutations (pink) are displayed below the graph. Dot plot shows the log distribution of drug sensitivity to PARP inhibitors (B) veliparib, (4D) olaparib, or (4F) cisplatin in the basal-like subtypes (BL=BL1+BL2), the mesenchymal-like subtypes (ML=M+MSL), and the LAR subtype. Black horizontal bars in the dot plot indicate the mean IC50 for each of the subtypes. *Statistically significant differences in IC50 values of BL compared with ML (P=0.017) and LAR(P=0.032), as determined by Mann-Whitney U test.

FIGS. 5A-5D: Differential sensitivity of the LAR TNBC subtype to AR and Hsp90 inhibitors. IC50 values for each TNBC cell line after treatment with (5A) bicalutamide or (5C) the Hsp90 inhibitor 17-DMAG for 72 hours. Black bar above bicalutamide indicates cell lines that failed to achieve an IC50. Heat map displays relative AR expression (log2) across TNBC cell lines. Dot plot shows log distribution of drug sensitivity to (5B) bicalutamide or (5D) 17-DMAG in the basal-like (BL=BL I+BL2), mesenchymal-like (ML=M+MSL), and LAR subtypes. Black horizontal bars in the dot plot indicate the mean IC50 for each of the subtypes. *Statistically significant differences in 1050 values of LAR versus BL (P=0.007) or ML (P=0.038) after bicalutamide and LAR versus BL and ML (P=0.05) after 17-DMAG treatments, as determined by Mann-Whitney U test.

FIGS. 6A-6D: Mesenchymal-like TNBC subtypes are sensitive to dasatinib and NVP-BEZ235. IC50 values for each TNBC cell lined treated with (6A) dasatinib or (6C) NVP-BEZ235 for 72 hours. Cell lines that have PIK3CA mutations (red) or are deficient in PTEN (blue, circle indicates mutated) are displayed below the NVP-BEZ235 graph. Dot plots show the log distribution of drug sensitivity to (6B) dasatinib or (6D) NVP-BEZ235 in the basal-like subtypes (BL=BL1+BL2), mesenchymal-like subtypes (ML=M+MSL), and LAR. Black horizontal bars in the dot plots indicate the mean 1050 for each of the subtypes. *Statistically significant differences in 1050 values of BL versus ML (P=0.020) when treated with dasatinib and ML versus BL (P=0.001) and LAR versus BL (P=0.01) when treated with NVP-BEZ235, as determined by Mann-Whitney U test.

FIG. 7: Xenograft tumors established from TNBC subtypes display differential sensitivity to cisplatin, bicalutamide, and NVP-BEZ235. Nude mice bearing established tumors (25-50 mm3) from basal-like (HCC 1806 and MDA-MB-468), LAR (SUM185PE and CAL-148), or mesenchymallike (CAL-51 and SUM159PT) were treated with cisplatin (red), bicalutamide (purple), NVP-BEZ235 (green), or vehicle (blue) for approximately 3 weeks. Serial tumor volumes (mm3) were measured at the indicated days. Each data point represents the mean tumor volume of 16 tumors; error bars represent SEM.

FIG. 8: Random distribution of TNBC subtypes found within dalasels. The percent of tumors in each cluster is displayed across 14 studies that comprise the training dataset.

FIG. 9: Consensus clustering of training and validation TNBC datasets (n=587). Heat map displays consensus clustering results depicting the robustness of sample classification. Red areas indicate samples that frequently cluster with each other over multiple iterations (1000) of k-means clustering (k::c 2 to k=9).

FIG. 10: Gene expression profiles derived from tumors that were laser-capture microdissecled represent all TNBC subtypes. Bar graph depicts the percentage of tumors that were microdissected (blue bars) present in the GSE584 (n=17) and Vanderbilt (n=14) datasets relative to non-microdissected tumors in the combined dataset (red bars).

FIGS. 11A-11B: TNBC subtypes identified by IHC. (11A) Silhouette plot showing the composition (n=number of tumors) and stability (AVG width) of k-means clustering on the TNBC training sel. Clusters with a silhouette width, s(i)>O were considered stable. (11B) Heatmap displays hierarchical clustering of ERBB2, PGR, ESR1 and AR expression in the tumors identified by IHC. Color bar identifies the cluster associated with each tumor.

FIG. 12: TNBC subtypes Identified by IHC display similar GE patterns to the six TNBC subtypes. IHC TNBC clusters are shown in silhouette plot with relative GE for genes unique to the six TNBC subtypes shown below.

FIG. 13: Differential GE across TNBC subtypes. Heatmaps show relative GE (log2, −2 to 2) associated with proliferation, DNA damage response, myoepithelial genes, immune signal transduction, TGFβ signaling, growth factor receptors, EMT, WNT signaling, stem-like, claudin (CL), angiogenesis, AR and of AR target genes across TNBC subtypes (as in FIG. 3).

FIGS. 14A-14B: TNBC tumor subtypes differentially stain for the proliferation marker Ki-67. (14A) Representative micrographs from 20 tumors showing IHC staining of the proliferation marker, Ki-67, in tumors from different TNBC subtypes. (14B) Dol plot showing the mean and distribution of Ki-67 staining within TNBC subtypes as scored by study pathologist. Subtypes: BL1=basal-like 1, BL2=basal-like 2, IM=immunomodulatory, M=mesenchymal-like, MSL=mesenchymal stem-like and LAR=luminal AR.

FIG. 15: Response rates differ across TNBC subtypes in taxane-treated patients. Percent of patients achieving pathologic complete response (pCR) after taxane-based treatment was significantly (P=0.042, chi-squared analysis) different for patients whose tumors correlated to basal-like (n=19), mesenchymal-like (n=16) and luminal AR (n=7) subtypes, from studies in which response data were available.

FIG. 16: 1M subtype Is enriched in Immune cell signaling. Heatmaps showing the relative GE (log2, −2 to 2) for genes involved in immune cell surface antigens, cytokines, immune cell signal transduction, complement. chemokine, and antigen presentation across TNBC subtypes (as in FIG. 3).

FIG. 17: The claudin-Iow predictor gene set identifies a sub-population of MSL tumors. Unsupervised hierarchical clustering was performed on the training TNBC tumors using genes (n=770) unique to the claud in•low subgroup [26]. Displayed to the right of the heatmap are the genes that are most differentially expressed (either high or low) in the claudin-Iow tumor set. Colorbar displays the TNBC subtype and heatmaps show relative levels (Log 2) 01 claudins (3, 4 and 7) and CD24, markers of this subgroup.

FIGS. 18A-18B: TNBC tumor subtypes differentially stain for AR by IHC. (18A) IHC staining for AR from 20 tumors with representative samples from each TNBC subtype shown. (18B) Dot plot showing the quantification of nuclear AR staining based on intensity and the percent of nuclei staining positive for AA in 20 tumors; Note, in some cases one dot represents overlapping dots from multiple tumors.

FIGS. 19A-19B: An androgen-inducible gene signature segregates LAR tumors. Hierarchical clustering was performed on both the (19A) training and (19) validation TNBC tumor sel using a 559 androgen-inducible gene signature (Hayes M J et al. Clin Cancer Res. 2008; 14(13):4038-4044).

FIGS. 20A-20B: TNBC subtypes differentially correlate with the intrinsic molecular subtypes. (20A) Healmaps show relative GE (log2, −2 to 2) of luminal and basal markers of breast cancer across all TNBC subtypes. (20B) Bar graph shows the distribution of intrinsic molecular subtypes of breast cancer (luminal A and B, normal breast-like, HER2, basal-like or unclassified) within each TNBC subtype (UNS=unstable, BL1=basal-like 1, Bl2=basal-like 2, 1M=immunomodulatory, M=mesenchymal-like, MSL=mesenchymal stem-like and LAR=luminal AR) as determined by best-fit Spearman correlation to the intrinsic centroids.

FIGS. 21A-21D TNBC subtypes differ in relapse-free survival and distant metastasis-free survival. Kaplan-Meier plot showing (21A) to-year RFS or (21C) DMFS in TNBC subtypes. RFS (21B) and DMFS (21D) hazard ratios (bold) and 95% CI (parentheses) for patients from TNBC subtypes. Shaded boxes indicate significant (P<0.05) comparisons.

FIGS. 22A-22B: TNBC subtypes differ in age, but are similar size upon diagnosis. Box plots show the median (horizontal line), range (rectangle) and SD (error bars) of (22A) age at diagnosis and (22B) tumor size (mm) between TNBC subtypes (as in FIG. 3); •P=9.0e−6

FIGS. 23A-23B: Chromosomal Aberrations in TNBC cell lines. (23A) Box plots depicting the average number of chromosomes (mode) in breast cancer cell lines correlating to basal-like (n=8) vs. mesenchymal-like (n=6) subtypes. (23B) Box plots depicting the average number of chromosomal rearrangements (translocations, inversions, and deletions) in basal-like vs. mesenchymal-like subtypes, Chromosome mode and rearrangements were obtained from Departments of Pathology and Oncology, Univ of Cambridge (www.path.cam.ac.uk/˜pawefish/cell%20line%20catalogues/breast-cell-lines.htm). *P<0.01 by unpaired t-test.

FIG. 24: TNBC cell lines cluster in three major groups: luminal AR, basal-like and mesenchymal-like. Unsupervised hierarchical clustering of TNBC cell lines performed on genes unique to TNBC subtypes (n=2188). Colorbar shows the best correlation of cell lines to the TNBC subtypes.

FIGS. 25A-25C: LAR cell lines depend on AR expression for colony formation. (25A) Top panel depicts relative AR mRNA levels obtained from GE microarrays performed on TNBC cell lines (log 2, centered on 0). Color bar identifies TNBC subtype classification for each cell line (immunomodulatory shown in orange and unclassified shown in red). Immunoblots showing relative expression AR protein in TNBC cell lines, Hsp90 serves as a loading control. (25B) AR expression 72 h following transfection with siRNA pools of non-targeting (NT) or targeting AR in MFM-223, MDA-MB-453 and SUM185PE cells. GAPDH expression serves as a loading control. (25C) Colony formation of MFM-223, MDA-MB-453 and SUM185PE cells 14d following siRNA transfection of AR or non-targeting control (NT).

FIGS. 26A-26B: Identification of PIK3CA mutations in AR-positive TNBC cell lines and tumors. (26A) Detection of PIK3CA 1047 mutation using digital droplet PCR. DNA from cell lines with varying PIK3CA status (HMEC=H1047R wt/wt, MDAMB453=H1047R wt/mut, SUM185=H1047R mut/mut and SUM159=H1047L wt/mut) were simultaneously amplified with fluorescent-conjugated primers to wild-type (VIC) or mutant (FAM) and the percentage of wt vs. mut DNA was measured by digital droplet PCR. DNA that did not undergo PCR amplification is indicated by no reaction (NR). (26B) Heatmap displays the TNBC molecular subtype based of TCGA samples with corresponding levels of AR RNA (RNA-seq) and protein (RPPA) for AR and phosphorylated AKT (T308 and S473). Color bar indicates PIK3CA mutations (red) within TNBC from the TCGA.

FIG. 27: AR-expressing TNBC cells display active PI3K pathway. Heatmap displays relative protein levels (RPPA) of AR, AKT (S473 and T308), GSK3β (S9 and S21) and PTEN across a large panel of TNBC cell lines. Hierarchical clustering was performed on cell lines and revel clusters of cell lines with active PI3K through PTEN loss or PIK3CA mutations.

FIGS. 28A-28C: AR-positive TNBC cell lines display active PI3K pathway and are sensitive to PI3K inhibitors. (28A) Immunoblot displays relative levels of AR, p-AKT, p-S6 in AR-dependent prostate cancer (LNCaP), human mammary epithelial cells (HMEC) and LAR TNBC, with GAPDH serving as a loading control. (28B) IHC-stained sections display cellular levels of AR, and p-AKT in cell lines from the same tissue microarray (TMA). (28C) Bar graphs display the 50% inhibitory concentration (IC₅₀) for TNBC cell lines treated with single-agent pan PI3K inhibitors (BKM-120 and GDC-0941) or PI3K/mTOR inhibitors (NVP-BEZ235 or GDC-0980) for 72 h. Black bars above graphs indicate cell lines in which the IC₅₀ was not reached at maximal dose. Bar below indicates normal HMEC cells and cell lines carrying PIK3CA mutations.

FIGS. 29A-29B: Genetic targeting of AR increases the efficacy of the PI3K inhibitor GDC-0941 and PI3K/mTOR inhibitor GDC-0980. (29A) Immunoblot displays decreased AR expression at 72 h following infection with two shRNAs targeting AR (shAR1 and shAR2) compared to infection with nontargeting shRNA (shNT) in three AR-positive TNBC cell lines. Actin levels below serve as loading controls. (29B) Line graphs display relative viability of LAR cell lines infected with nontargeting (shNT) or shRNAs targeting AR (shAR1 and shAR2) following a 72 h treatment with the pan-PI3K inhibitor GDC-0941 (top) or the dual PI3K/mTOR inhibitor GDC-0980.

FIGS. 30A-30B: Pharmacological targeting of AR with bicalutamide increases the efficacy of GDC0941 and GDC0980 in AR-expressing TNBC. (30A) Line graphs show relative viability of AR-expressing cell lines treated with increasing doses of GDC-0941 (top) or GDC-0980 (bottom) alone or in combination with 25 μM bicalutamide (CDX). Dashed black line depicts the theoretical line of additivity of both drugs determined from the effect of bicalutamide alone and either GDC-0941 or GDC-0980 alone. (30B) Immunoblots from three AR-expressing TNBC cell lines treated with either bicalutamide (CDX), GDC-0941, GDC0980 alone or bicalutamide in combination with either GDC-0941 or GDC-0980 for 24 h or 48 h were probed for AR, PARP, p-AKT, AKT, p-S6, S6 and GAPDH.

FIGS. 31A-31B: Combined inhibition of AR and PI3K increases apoptotic cell death in AR+ TNBC cell lines. (31A) Bar graphs display relative caspase 3/7 activity (RLU) normalized to viable cell number 48 hrs after treatment with vehicle, positive control (3 μM adriamycin, ADR), 50 μM bicalutamide (CDX) and 3 μM GDC-0941 or 1 μM GDC-0980 alone or in combination with CDX. (31B) Histograms show representative cell cycle analysis of MDA-MB-453 cells treated with similar conditions as above. Indicated percentages represent the fraction of hypodiploid DNA (sub-G1), indicative of late stage apoptotic DNA fragmentation.

FIGS. 32A-32C: Simultaneous targeting of AR and PI3K decreases viability of AR-expressing cell lines grown in a 3-D forced suspension assay and inhibits in vivo xenograft growth. (31A) Representative images display 3-D cell aggregates of MDA-MB-453 cells treated with increasing doses of GDC-0941 or GDC-0980 in the absence or presence of 25 μM bicalutamide (CDX). (32B) Line graphs display relative viability of 3-D cell aggregates treated with GDC-0941 or GDC-0980 alone or in combination with 25 μM bicalutamide (CDX). Dashed black line depicts the theoretical line of additivity determined from the effect of bicalutamide alone and either GDC-0941 or GDC-0980 alone. (32C) Nude mice bearing established tumors from AR-positive TNBC cell lines (CAL-148 and MDA-MB-453) were treated with either bicalutamide (CDX, black hashed line), NVP-BEZ235, GDC-0980 or with the combination of bicalutamide and either NVP-BEZ235 (blue hashed line) or GDC-0980 (red hashed line). Serial tumor volumes (mm³) were measured at the indicated days. Each data point represents mean tumor volume of 16 tumors; error bars represent SEM.

FIGS. 33A-33B: Detection of PIK3CA mutations by Sanger and digital droplet PCR. (33A) Electropherograms display representative results from sanger sequencing of the E20 amplicon in a PIK3CA wild-type (top) or a H1047R PIK3CA mutant sample. (33B) Scatterplot shows the percent of cells with mutant PIK3CA detected by digital droplet compared to Sanger sequencing.

FIG. 34: Genetic targeting of AR increases the efficacy of the PI3K inhibitor BKM-120 and PI3K/mTOR inhibitor NVP-BEZ235. Line graphs display relative viability of LAR cell lines infected with nontargeting (shNT) or shRNAs targeting AR (shAR1 and shAR2) following a 72 h treatment with the pan-PI3K inhibitor BKM-120 (top) or the dual PI3K/mTOR inhibitor NVP-BEZ235.

FIG. 35: Pharmacological targeting of AR with bicalutamide increases the efficacy of BKM120 and NVP-BEZ235 in AR-expressing TNBC. Line graphs show relative viability of AR-expressing cell lines treated with increasing doses of BKM120 (top) or NVP-BEZ235 (bottom) alone or in combination with 25 μM bicalutamide (CDX). Dashed black line depicts the theoretical line of additivity determined from the effect of bicalutamide alone and either BKM120 or NVP-BEZ235 alone.

FIGS. 36A-36B: Simultaneous targeting of AR and PI3K decreases viability of AR-expressing cell lines grown in a 3-D forced suspension assay. (36A) Line graphs display relative viability of 3-D cell aggregates treated with BKM120 or NVP-BEZ235 alone or in combination with 25 uM bicalutamide (CDX). Dashed black line depicts the theoretical line of additivity determined from the effect of bicalutamide alone and either BKM120 or NVP-BEZ235 alone. (36B) Immunoblots from three AR-expressing TNBC cell lines treated with either bicalutamide (CDX), BKM-120, BEZ235 alone or in combination with bicalutamide for 24 h or 48 h. Western blots were probed for AR, PARP, p-AKT, AKT, p-S6, S6 and GAPDH.

FIG. 37: Combined Targeting of PI3K and AR increase apoptosis detected by annexin V and propidium iodide (PI) staining. Scattergrams show the percentage of viable (lower left quadrant, annexin V and PI negative), early apoptotic (lower right quadrant, annexin V-positive and PI-negative), or late apoptotic/necrotic (upper right quadrant, annevin V and PI positive) cells following 48 hrs of treatment with either GDC-0941 or GDC-0980 alone or in combination with 50 μM bicalutamide (CDX).

FIGS. 38A-38C: Genetic and pharmacological targeting of AR increases p-AKT.

FIG. 39: PDGFR inhibition selectively inhibits viability of mesenchymal-like TNBC cell lines. Bar graph displays the half-maximal inhibitory concentration (nM) of the PDGFR inhibitor sorafenib for a panel of TNBC cell lines. Colorbar below designates the TNBC subtype (basal-like=black, mesenchymal-like=grey) or normal cells (white).

FIG. 40: IGF1R inhibition selectively inhibits viability of mesenchymal-like TNBC cell lines. Bar graph displays the half-maximal inhibitory concentration (nM) of the IGF1R inhibitor OSI-906 for a panel of TNBC cell lines. Colorbar below designates the TNBC subtype (basal-like=black, mesenchymal-like=grey) or normal cells (white).

FIG. 41: IGF1R inhibition selectively inhibits viability of mesenchymal-like TNBC cell lines. Bar graph displays the half-maximal inhibitory concentration (nM) of the IGF1R inhibitor BMS-754807 for a panel of TNBC cell lines. Colorbar below designates the TNBC subtype (basal-like=black, mesenchymal-like=grey) or normal cells (white).

FIG. 42: MET inhibition selectively inhibits viability of mesenchymal-like TNBC cell lines. Bar graph displays the half-maximal inhibitory concentration (nM) of the MET inhibitor PF2341066 for a panel of TNBC cell lines. Colorbar below designates the TNBC subtype (basal-like=black, mesenchymal-like=grey) or normal cells (white).

DETAILED DESCRIPTION OF THE INVENTION

Triple-negative breast cancer (TNBC) is a highly diverse group of cancers, and subtyping is necessary to better identify molecular-based therapies. In this study, gene expression (GE) profiles from 21 breast cancer data sets were analyzed and 587 TNBC cases were identified. Cluster analysis identified 6 TNBC subtypes displaying unique GE and ontologies, including 2 basal-like (BL1 and BL2), an immunomodulatory (IM), a mesenchymal (M), a mesenchymal stem-like (MSL), and a luminal androgen receptor (LAR) subtype. Further, GE analysis allowed identification of TNBC cell line models representative of these subtypes. Predicted “driver” signaling pathways were pharmacologically targeted in these cell line models as proof of concept that analysis of distinct GE signatures can inform therapy selection. BL1 and BL2 subtypes had higher expression of cell cycle and DNA damage response genes, and representative cell lines preferentially responded to cisplatin. M and MSL subtypes were enriched in GE for epithelial-mesenchymal transition, and growth factor pathways and cell models responded to NVP-BEZ235 (a PI3K/mTOR inhibitor) and dasatinib (an abl/src inhibitor). The LAR subtype includes patients with decreased relapse-free survival and was characterized by androgen receptor (AR) signaling. LAR cell lines were uniquely sensitive to bicalutamide (an AR antagonist). These data provide biomarker selection, drug discovery, and clinical trial design that align TNBC patients to appropriate targeted therapies.

An extensive number of TNBC GE profiles was compiled with the intent of molecularly subtyping the disease. Six (6) TNBC subtypes were identified. Further, using GE signatures derived from each TNBC subtype, representative TNBC cell lines that serve as models for the different subtypes of the disease were aligned. Using the panel of cell lines, prominent signaling pathways revealed by GE signatures were pharmacologically targeted and it was found that the cell lines representing the various subtypes had different sensitivities to targeted therapies currently under laboratory and clinical investigation. The identification of diverse TNBC subtypes and the molecular drivers in corresponding cell line models provides great insight to the heterogeneity of this disease and provides preclinical platforms for the development of effective treatment (see Lehmann, B. D., et al., J Clin Invest, 121(7):2750-2767 (July 2011), the entire teachings of which are incorporated herein by reference).

Also described herein is further investigation of a panel of AR-positive TNBC tumors which showed that PIK3CA kinase mutations are a frequent event in the LAR subtype (65.3% vs. 38.4%) and were not just selected for in vitro during establishment of the tumor-derived cell lines. Also shown herein is that PI3K pathway activation plays a role in resistance to AR antagonists, as there are elevated levels of activated AKT in residual tumors after bicalutamide treatment of xenograft tumors. Further, it was found that genetic or pharmacological targeting of AR synergizes with PI3K/mTOR inhibition in both two- and three-dimensional cell culture models. Based on the cell culture-based results, the combination of these inhibitors in in vivo xenograft studies was examined using bicalutamide+/−GDC0980 or NVP-BEZ235. The preclinical data herein provide the rationale for pre-selecting AR-positive TNBC patients for treatment with the combination of AR antagonists and/or PI3K/mTOR inhibitors.

As discussed herein, triple negative breast cancer (TNBC) refers to breast cancers that are estrogen receptor (ER) negative, progesterone receptor (PR) negative and human epidermal growth factor receptor 2 (HER-2) negative. The invention is based, in part, of the discovery of six TNBC subtypes.

Accordingly, in one aspect provided herein are methods of determining a triple negative breast cancer (TNBC) subtype in an individual in need thereof comprising determining expression of one or more genes (e.g., presence of one or more mRNAs and/or protein encoded by gene) in one or more TNBC cells of the individual; and comparing the expression of the one or more genes in the TNBC cells with the expression of the one or more genes in a control. Increased expression of one or more genes comprising one or more cell cycle genes, cell division genes, proliferation genes, DNA damage response genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC BL1 subtype. Increased expression of one or more growth factor signaling genes, glycolysis genes, gluconeogenesis genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC BL2 subtype. Increased expression of one or more immune cell signaling genes, cytokine signaling genes, antigen processing and presentation genes, core immune signal transduction genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC IM subtype. Increased expression of one or more cell motility genes, extracellular matrix (ECM) receptor interaction genes, cell differentiation genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC M subtype. Increased expression of one or more cell motility genes, cellular differentiation genes, growth pathway genes, growth factor signaling genes, angiogenesis genes, immune signaling genes, stem cell genes, HOX genes, mesenchymal stem cell-specific marker genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC MSL subtype. Increased expression of one or more hormone regulated genes in the TNBC cells compared to the control indicates that the TNBC is a TNBC LAR type.

In a particular aspect, the invention is directed to a method of determining a TNBC BL1 subtype in an individual in need thereof comprising determining increased expression of one or more cell cycle genes, cell division genes, proliferation genes, DNA damage response genes or a combination thereof in the TNBC cells of the individual compared to the control. Increased expression of the one or more genes indicates that the TNBC is a BL1 subtype TNBC. In one aspect, the method of determining a TNBC BL1 subtype in an individual in need thereof comprises selectively detecting increased expression of a gene combination comprising AURKA, AURKB, CENPA, CENPF, BUB1, BUB1B, TTK, CCNA2, PLKJ, PRC1, MYC, NRAS, PLK1, BIRC5, CHEK1, FANCA, FANCG, FOXM1, HNGA1, RAD54BP, RAD51, NEKS, NBN, EXO1, MSH2, MCM10, RAD21, SIX3, Z1C1, SOX4, SOX1 and MDC1 wherein detection of increased expression of the gene combination indicates that the TNBC is TNBC BL1 subtype. Determination that the TNBC is a TNBC BL1 subtype can further comprise detecting increased expression of Ki-67 mRNA in the TNBC cells compared to the control. In addition, determination that the TNBC is a TNBC BL1 subtype can further comprise detecting one or more mutated genes. Examples of such mutated genes include mutated BRCA1, STAT4, UTX, BRCA2, TP53, CTNND1, TOP2B, CAMK1G, MAPK13, MDC1, PTEN, RB1, SMAD4, CDKN2A, ATM, ATR, CLSPN, HDAC4, NOTCH1, SMARCAL1, and TIMELESS.

In another aspect, the invention is directed to a method of determining a TNBC BL2 subtype in an individual in need thereof comprising determining increased expression of one or more growth factor signaling genes, glycolysis genes, gluconeogenesis genes or a combination thereof in the TNBC cells compared to the control. Increased expression of the one or more genes indicates that the TNBC is a TNBC BL2 subtype. In one aspect, the method of determining a TNBC BL subtype in an individual in need thereof comprises selectively detecting increased expression of a gene combination comprising EGFR, MET, ELF4, MAF, NUAK1, JAG1, FOSL2, 1D1, ZIC1, SOX11, 1D3, FHL2, EPHA2, TP63 and MME wherein detection of increased expression of the gene combination indicates that the TNBC is TNBC BL2 subtype. Determination that the TNBC is a TNBC BL2 subtype can further comprise detecting one or more mutated genes. Examples of such genes comprise mutated BRCA1, RB1, TP53, PTEN, CDKN2A, UTX, BRAC2, PTCH1, PTCH2, and RET.

In another aspect, the invention is directed to a method of determining a TNBC M subtype in an individual in need thereof comprising determining increased expression of one or more cell motility genes, extracellular matrix (ECM) receptor interaction genes, cell differentiation genes or a combination thereof in the TNBC cells compared to the control. Increased expression of the one or more genes indicates that the TNBC is a TNBC M subtype. In one aspect, the method of determining a TNBC M subtype in an individual in need thereof comprises selectively detecting increased expression of a gene combination comprising TGFB1L1, BGN, SMAD6, SMAD7, NOTCH1, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TGFBR3, MMP2, ACTA2, SNAI2, SPARC, SMAD7, PDGFRA, TAGLN, TCF4, TWIST1, ZEB1, COL3A1, JAG1, EN1, MYLK, STK38L, CDH11, ETV5, IGF1R, FGFR1, FGFR2, FGFR3, TBX3, COL5A2, GNG11, ZEB2, CTNNB1, DKK2, DKK3, SFPR4, TCF4, TCF7L2, FZD4, CAV1, CAV2, CCND1 and CCND2 wherein detection of increased expression of the gene combination indicates that the TNBC is TNBC M subtype. Determination that the TNBC is a TNBC M subtype can further comprise detecting decreased E-cadherin (CDH1) expression compared to the control. Determination that the TNBC is a TNBC M subtype can further comprise detecting one or more mutated genes. Examples of such mutated genes include mutated PTEN, RB1, TP53, PIK3CA, APC, BRAF, CTNNB1, FGFR1, GLI1, HRAS, KRAS, NOTCH1, and NOTCH4. Determination that the TNBC is a TNBC M subtype can further comprise detecting chromosomal amplifications in KRAS, IGF1R or MET.

In another aspect, the invention is directed to a method of determining a TNBC MSL subtype in an individual in need thereof comprising determining increased expression of one or more cell motility genes, cellular differentiation genes, growth pathway genes, growth factor signaling genes, angiogenesis genes, immune signaling genes, stem cell genes, HOX genes, mesenchymal stem cell-specific marker genes or a combination thereof in the TNBC cells compared to the control. Increased expression of the one or more genes indicates that the TNBC is a TNBC MSL subtype. In one aspect, the method of determining a TNBC MSL subtype in an individual in need thereof comprises selectively detecting increased expression of a gene combination comprising VEGFR2 (KDR), TEK, TIE1, EPAS1, ABCA8, PROCR, ENG, ALDHA1, PER1, ABCB1, TERF21P, BCL2, BMP2, EPAS1, STAT4, PPARG, JAK1, ID1, SMAD3, TWIST1, THY1, HOXA5, HOXA10, GL13, HHEX, ZFHX4, HMBOX1, FOS, PIK3R1, MAF, MAFB, RPS6KA2, TCF4, TGFB1L1, MEIS1, MEIS2, MEOX1, MEOX2, MSX1, ITGAV, KDR, NGFR, NT5E, PDGFRA, PDGFRB, POU2F1, and VCAM1 wherein detection of increased expression of the gene combination indicates that the TNBC is TNBC MSL subtype. Determination that the TNBC is a TNBC MSL subtype can further comprise detecting low expression of claudins 3, 4, 7 or a combination thereof compared to the control. Determination that the TNBC is a MSL subtype TNBC can further comprise detecting one or more mutated genes. Examples of such mutated genes include mutated CDKN2A, HRAS, TP53, NF1, PIK3CA, BRCA1, BRAF, KRAS, NF2, PDGFRA, APC, CTNNB1, FGFR1, PDGFRB.

In another aspect, the invention is directed to a method of determining a TNBC IM subtype in an individual in need thereof comprising determining increased expression of one or more immune cell signaling genes, cytokine signaling genes, antigen processing and presentation genes, core immune signal transduction genes or a combination thereof in the TNBC cells compared to the control. Increased expression of the one or more genes indicates that the TNBC is a TNBC IM subtype. In one aspect, the method of determining a TNBC IM subtype in an individual in need thereof comprises selectively detecting increased expression of a gene combination comprising CCL19, CCL3, CCL4, CCL5, CCL8, CCR1, CCR2, CCR5, CCR7, CD2, CD37, CD38, CD3D, CD48, CD52, CD69, CD74, and CD8A wherein detection of increased expression of the gene combination indicates that the TNBC is TNBC IM subtype. Determination that the TNBC is a TNBC IM subtype can further comprise detecting one or more mutated genes. Examples of such mutated genes include TP53, CTNNA1, DDX18, HUWE1, NFKBIA, APC, BRAF, MAP2K4, RB1, STAT4, STAT1, and RET.

In another aspect, the invention is directed to a method of determining a TNBC LAR subtype in an individual in need thereof comprising determining increased expression of one or more hormone regulated genes in the TNBC cells compared to the control. Increased expression of the one or more genes indicates that the TNBC is a TNBC LAR type. In one aspect, the method of determining a TNBC LAR subtype in an individual in need thereof comprises selectively detecting increased expression of a gene combination comprising AR, DHCR24, ALCAM, GATA2, GATA3, IDIH1, IDIH2, CDH11, ERBB3, CUX2, FGFR4, HOPX, FASN, FKBP5, APOD, PIP, SPDEF, CLDN8, FOXA1, KRT18, and XBP1 wherein detection of increased expression of the gene combination indicates that the TNBC is TNBC LAR subtype. Determination that the TNBC is a LAR subtype TNBC can further comprise detecting one or more mutated genes. Examples of such mutated genes include PIK3CA, CDH1, PTEN, RB1, TP53, and MAP3K1.

A variety of methods (e.g. spectroscopy, colorometry, electrophoresis, chromatography) can be used to detect increased expression of a (one or more) gene. As is apparent to those of skill in the art, increased expression of one or more genes can be detected by measuring all or a portion of nucleic acid (e.g., DNA, mRNA) of the gene and/or protein (polypeptide) expressed by the gene. The level, expression and/or activity of a gene and or its encoded polypeptide can be measured. For example, nucleic acid such as genes, mRNA or a combination thereof, can be determined using PCR (e.g., RT-PCR, RT-qPCR), gene chips or microarray analysis (DNA arrays, gene expression arrays, nanostrings), next generation sequencing (e.g., next generation RNA sequencing), in situ hybridization, blotting techniques, and the like. Protein can be detected using immunoassays (e.g., immunohistochemistry, immunofluorescence, immunoprecipitation), arrays (e.g., reverse phase protein microarrays), blotting techniques (e.g., Western blots), SDS-PAGE, and the like

As described herein, the methods can further comprise detecting one or more mutated genes. A variety of methods can be used to detect one or more mutated genes. Examples of such methods include a SNaPshot assay, exome sequencing, sanger gene sequencing, resequencing array analysis, mRNA analysis/cDNA sequencing polymerase chain reaction (PCR), single-strand conformation polymorphism (sscp), heteroduplex analysis (het), allele-specific oligonucleotide (aso), restriction fragment analysis, allele-specific amplification (asa), single nucleotide primer extension, oligonucleotide ligation assay (ola), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and single strand conformation polymorphism (SSCP).

The methods can further comprise comparing the expression of the one or more genes in the individual to the expression of the one or more genes in a control. As will be apparent to those of skill in the art, a variety of suitable controls can be used. Examples of such controls include one or more non-cancer cells (e.g., breast cells from one or more individuals that do not have cancer) and/or non-TNBC cells (e.g., from the individual being tested). The control can also be a (one or more) standard or reference control established by assaying one or more (e.g., a large sample of) individuals which do not have cancer (e.g., TNBC) and using a statistical model to obtain a control value (standard value; known standard). See, for example, models described in Knapp, R. G. and Miller M. C. (1992) Clinical Epidemiology and Biostatistics, William and Wilkins, Harual Publishing Co. Malvern, Pa., which is incorporated herein by reference.

As used herein an “individual” refers to an animal, and in a particular aspect, a mammal. Examples of mammals include primates, a canine, a feline, a rodent, and the like. Specific examples include humans, dogs, cats, horses, cows, sheep, goats, rabbits, guinea pigs, rats and mice.

The term “individual in need thereof” refers to an individual who is in need of treatment or prophylaxis as determined by a researcher, veterinarian, medical doctor or other clinician. In one aspect, an individual in need thereof is a mammal, such as a human. In other aspects, the individual has been diagnosed with breast cancer, the individual has not been diagnosed with breast cancer, or the individual is at risk of developing breast cancer.

The methods of the invention can further comprise detecting expression (increased expression) of one or more genes in a sample (biological sample) of the individual. Thus, the method can further comprise obtaining a (one or more) sample from the individual. The sample can be, for example, a biological fluid, a biological tissue (e.g., a biopsy) and combinations thereof from the individual, hi particular aspects, the sample is one or more TNBC cells (e.g., epithelial cells, mesenchymal cells, immune cells). Methods for obtaining such biological samples from an individual are known to those of skill in the art.

As also shown herein, the methods can further comprise determining a treatment protocol for the triple negative breast cancer (TNBC) patient based on the TNBC subtype. As described herein, a “cancer therapy”, “treatment for cancer” or “cancer treatment” comprises administering one or more agents to the individual. In one embodiment, the agent is a chemotherapeutic agent which targets the TNBC cells. Examples of such agents include an alkylating agent (e.g., busulfan, cisplatin, carboplatin, chlorambucil, cyclophosphamide, ifosfamide, dacarbazine (DTIC), mechlorethamine (nitrogen mustard), melphalan, temozolomide); a nitrosoureas (e.g., carmustine (BCNU), lomustine (CCNU)); an antimetabolite (e.g., 5-fluorouracil, capecitabine, 6-mercaptopurine, methotrexate, gemcitabine, cytarabine (ara-C), fludarabine, pemetrexed); an anthracycline or related drug (e.g., daunorubicin, doxorubicin (adriamycin), epirubicin, idarubicin, mitoxatrone); a topoisomerase (topoisomerase I inhibitor; topoisomerase inhibitor II) inhibitor (e.g., topotecan, irinotecan, etoposide (VP-16), teniposide); and a mitotic inhibitor (e.g., taxanes (paclitaxel, docetaxel, taxol) vinca alkaloids (vinblastine, vincristine, vinorelbine).

In another embodiment, the agent is a targeted therapy agent which attacks cancer cells more specifically than chemotherapeutic agents. Examples of such agents include imatinib (Gleevec), gefitinib (Iressa), erlotinib (Tarceva), rituximab (Rituxan), and bevacizumab (Avastin). In yet another embodiment, the agent is a sex hormone, or hormone-like drug that alters the action or production of female or male hormones and can be used to slow the growth of breast, prostate, and endometrial (uterine) cancers. Examples of such agents include anti-estrogens (e.g., tamoxifen, fulvestrant), aromatase inhibitors (e.g., anastrozole, exemestane, letrozole), progestins (e.g., megestrol acetate), anti-androgens (e.g., bicalutamide, flutamide) and LHRH agonists (leuprolide, goserelin). In addition, the agent can be a drug which is used to stimulate the immune system to more effectively recognize and attack cancer cells of an individual with cancer. Other examples of agents include a hormone such as a selective estrogen receptor modulator (SERM); an antibody or antigen binding fragment thereof (e.g., herceptin); a protein tyrosine kinase inhibitor; a combination of chemotherapeutic agents such as cytoxan (C), methotrexate (M), fluorouracil (F), an anthracylcin such as adriamycin (A), epirubicin (E), doxorubicin, and/or daunorubicin; a targeted kinase inhibitor; a metalloproteinase inhibitor; and a proteosome inhibitor.

The one or more agents can be administered to the individual before (e.g., neoadjuvant therapy), during or after (e.g., adjuvant therapy) primary treatment of the cancer. As used herein “primary treatment of a cancer” generally refers to a treatment involving surgery (e.g., surgical removal of a tumor) and/or radiation (e.g., local radiation). In the methods of the present invention, the “treatment for cancer” can be a neoadjuvant treatment wherein an agent (e.g., a hormone, a chemotherapeutic) is administered prior to surgical removal of a (residual) tumor, or prior to localized radiation (e.g., radiation used to shrink the tumor in order to simplify subsequent surgical removal of the tumor). In another embodiment, the “treatment for cancer” can be an adjuvant treatment wherein an agent (e.g., a hormone, a chemotherapeutic agent) is administered after surgical removal of a (residual) tumor, or after localized radiation. In yet another embodiment, the treatment can be a palliative treatment in which one or more chemotherapeutic agents are administered to an individual to treat metastatic cancer (e.g., to make the individual more comfortable and/or to prolong survival of the individual after the cancer has metastasized).

In particular aspects, the TNBC 13L1 or BL2 subtype is detected in the individual and the individual is treated with one or more drugs that damages DNA. Examples of such drugs include an alkylating-like agent (e.g., cisplatin) and a PARP inhibitor (e.g., veliparib, olaparib).

In another aspect, the TNBC ML subtype is detected in the individual and the individual is treated with one or more drugs that inhibits Src (e.g., disatinib), IGF1R (e.g., OSI-906, BMS-754807), MET (e.g., PF2341066), PDGFR (e.g., sorafinib), PI3K (e.g., BKM-120, GDC0941), P 13K/mTOR (e.g., NVP-BEZ235, GDC0980) or a combination thereof.

In another aspect, the TNBC LAR subtype is detected in the individual and the individual is treated with one or more drugs that inhibit androgen receptor (AR). Examples of such drugs include bicalutamide, MVD3100, and abiraterone. The method can further comprise treating the individual with P 13K/mTOR (e.g., NVP-BEZ235, GDC0980) or a combination thereof. The method can further comprise treating the individual with an inhibitor of HSP90 (e.g., DMAG).

In other aspects, the invention can further comprise predicting whether an individual (e.g., patient) will benefit from a (one or more) treatment for a particular TNBC subtype.

Also described herein are TNBC cell lines that serve as models for each of the six TNBC subtypes. Thus, in another aspect, the invention is directed to a method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) subtype comprising contacting a cell line that is a model for the TNBC subtype of interest with an agent to be assessed; and determining viability of the cell line in the presence of the agent, wherein if the viability of the cell line decreases in the presence of the agent, then the agent can be used to treat the TNBC subtype of interest. The TNBC subtype of interest can be a TNBC BL-1 subtype, a TNBC BL-2 subtype, a TNBC IM subtype, a TNBC M subtype, a TNBC MSL subtype or a TNBC LAR subtype. In addition, as will be apparent to those of skill in the art, the viability of a cell decreases when e.g., the cell undergoes apoptosis, proliferation of the cell is inhibited or slowed and/or metastasis of the cell is inhibited to slowed.

Examples of agents (test agent; agent of interest) include nucleic acids, polypeptides, fusion proteins, peptidomimetics, prodrugs, drugs, receptors, binding agents (e.g., antibodies), small molecules, etc and libraries (e.g., combinatorial libraries) of such agents. Test agents can be obtained made or obtained from libraries of natural, synthetic, and/or semi-synthetic products (e.g., extracts). Those skilled in the field of drug discovery and development will understand the precise source of such agents.

In one aspect, the invention is directed to a method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) BL-1 subtype comprising contacting one or more TNBC BL-1 subtype cell lines with an agent to be assessed. The viability of the one or more cell lines in the presence of the agent is detected, wherein if the viability of the one or more cell lines decreases in the presence of the agent, then the agent can be used to treat the TNBC BL-1 subtype. Examples of TNBC BL-1 subtype cell lines include HCC2157, HCC1599, HCC1937, HCC1143, HCC3153, MDA-MB-468, and HCC38.

In another aspect, the invention is directed to a method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) BL-2 subtype comprising contacting one or more TNBC BL-2 subtype cell lines with an agent to be assessed. The viability of the one or more cell lines in the presence of the agent is determined, wherein if the viability of the one or more cell lines decreases in the presence of the agent, then the agent can be used to treat the TNBC BL-2 subtype. Examples of TNBC BL-2 subtype cell lines include SUM149PT, CAL-851, HCC70, HCC1806 and HDQ-P1.

In another aspect, the invention is directed to a method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) IM subtype comprising contacting one or more TNBC IM subtype cell lines with an agent to be assessed. The viability of the one or more cell lines in the presence of the agent is determined, wherein if the viability of the one or more cell lines decreases in the presence of the agent, then the agent can be used to treat the TNBC IM subtype. Examples of TNBC IM subtype cell lines include HCC1187 and DU4475.

In another aspect, the invention is directed to a method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) M subtype comprising contacting one or more TNBC M subtype cell lines with an agent to be assessed. The viability of the one or more cell lines in the presence of the agent is determined, wherein if the viability of the one or more cell lines decreases in the presence of the agent, then the agent can be used to treat the TNBC M subtype. Examples of TNBC M subtype cell lines include BT-549, CAL-51 and CAL-120.

In another aspect, the invention is directed to a method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) MSL subtype comprising contacting one or more TNBC MSL subtype cell lines with an agent to be assessed. The viability of the one or more cell lines in the presence of the agent is determined, wherein if the viability of the one or more cell lines decreases in the presence of the agent, then the agent can be used to treat the TNBC MSL subtype. Examples of TNBC MSL subtype cell lines include HS578T, MDA-MB-157, SUM159PT, MDA-MB-436, and MDA-MB-231.

In another aspect, the invention is directed to a method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) LAR subtype comprising contacting one or more TNBC LAR subtype cell lines with an agent to be assessed. The viability of the one or more cell lines in the presence of the agent is determined, wherein if the viability of the one or more cell lines decreases in the presence of the agent, then the agent can be used to treat the TNBC LAR subtype. Examples of TNBC LAR subtype cell lines include MDA-MB, SUM185PE, HCC2185, CAL-148, and MFM-223.

In the methods of the invention, viability of one of more of the cells can be determined using a variety of methods. Examples of such methods include a membrane leakage assay, a mitochondrial activity assay, a functional assay, a proteomic assay, a genomic assay or a combination thereof.

The methods can further comprise comparing the viability of the one or more cell lines in the presence of the agent to the viability of a control such as a non-cancerous cell line (e.g., a culture of normal human and immortalized MCF210A).

EXEMPLIFICATION Example 1 Identification of Human Triple Negative Breast Cancer Subtypes and Models for Selection of Targeted Therapies Methods

Laser capture microdissection, RNA extraction, and GE profiling. Invasive tumor cells from serial sections of primary breast cancers (n=112) were captured onto polymeric caps using the PixCell II lasercapture microdissection system (Arcturus) as previously described (Bauer J A, et al. Clin Cancer Res. 2010; 16(2):681-690). Areas of ductal carcinoma in situ and normal breast tissue were excluded and areas of inflammation and areas with tumor-associated fibroblasts were avoided. Total RNA was isolated from captured cells, quantified, and integrity analyzed, and microarray analyses were done using Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays as previously described (Bauer J A, et al. Clin Cancer Res. 2010; 16(2):681-690).

Data set collection and TNBC identification by bimodal filtering. 2353 human breast cancer GE profiles were compiled from 14 publicly available breast cancer microarray data sets (GEO, www.ncbi.nlm.nih.gov/gds; Array Express, www.ebi.ac.uk/microarray-as/ae/) including 112 primary breast cancer GE profiles from our institution (Vanderbilt University Medical Center). All Vanderbilt tissue samples were taken from individuals treated at Vanderbilt University with institutional review board approval, and all patients signed a protocol-specific consent. All GE profiles were generated on Affymetrix microarrays and collected for identification of TNBCs for the training data set (Table 1). An additional 894 breast cancer GE profiles from 7 data sets were collected for the identification of TNBCs for the validation data set (Table 2). Raw GE values for each data set (n 21) were normalized independently using RMA procedure. The Affymetrix probes 205225_at, 208305_at and 216836_s_at were chosen to represent ER, PR, and HER2 expression, respectively (Karn T, et al. Breast Cancer Res Treat. 2010; 120(3):567-579). For each data set, empirical expression distributions of ER, PR, and HER2 were analyzed using a 2-component Gaussian mixture distribution model and parameters were estimated by maximum likelihood optimization, using optim function (R statistical software, www.r-project.org). The posterior probability of negative expression status for ER, PR, and HER2 was then estimated. A sample was classified as having negative expression if its posterior probability was less than 0.5. Upon initial hierarchical clustering, it was evident that some samples were from the same tumors, but in different data sets. These and additional outliers were removed after PCA. To ensure all ER/PR/HER2-positive tumors were removed, a secondary filter was performed on the combined samples identified by bimodal filtering. TNBC tumors were renormalized along with 5 positive controls for each parameter (ER, PR, and HER2) from 4 data sets that were positive by IHC and expressed mRNA near the center of the positive bimodal peak (FIG. 1B). Only tumors that displayed a greater than 10-fold reduction in expression than the positive controls were considered negative in expression and used for further analysis, resulting in 386 TNBC tumors (training set) and 201 TNBC tumors (validation set).

Normalization, data reduction, and cross-platform batch effect removal. Training (n=386) and validation (n=201) TNBC data sets identified by the 2-component Gaussian distribution model were collectively RMA normalized, summarized and log-transformed using the combined raw GE from each data set. For genes containing multiple probes, the probe with the largest interquartile range across the samples was chosen to represent the gene. Batch effects were removed by fitting each gene to a linear model with 14 and 7 fixed effects for each data set, respectively. The residual genes from this model (n=13,060) were used for subsequent clustering analysis.

GE-based identification of TNBC subtypes. k-means clustering and consensus clustering were used to determine the optimal number of stable TNBC subtypes. Cluster robustness was assessed by consensus clustering using agglomerative k-means clustering (1,000 iterations), with average linkage on the 386 TNBC profiles using the most differentially expressed genes (SD>0.8; n=1510 genes) (Gene Pattern version 3.2.1, GSE-A, www.broadinstitute.org/gsea/) (19). The optimal number of clusters was determined from the CDF, which plots the corresponding empirical cumulative distribution, defined over the range [0,1], and from calculation of the proportion increase in the area under the CDF curve. The number of clusters is decided when any further increase in cluster number (k) does not lead to a corresponding marked increase in the CDF area. PCA and heat maps were generated using Genespring GX ver.10 software (Agilent).

Functional annotation. Each TNBC subtype was tested for gene enrichment compared with all other samples using GSE-A software (Subramanian A, et al. Proc Natl Acad Sci USA. 2005; 102(43):15545-15550). Genes were tested for enrichment in the C2 curated gene sets of canonical pathways. Using the GSE-A algorithm (1,000 permutations), the top significantly enriched canonical pathways were selected based on a normalized enrichment score (NES) greater than 0.4 and false discovery rate (FDR) q value of less than 0.60. The FDR cutoff of 0.60 was chosen because of the lack of coherence in the data set collection spanning 21 studies, and more stringent FDR cutoffs resulted in fewer results, potentially overlooking significant pathways.

TNBC subtype gene signature derivation. The 20% of genes with the highest and lowest expression levels in at least 50% of the samples for each subtype were chosen for further analysis. Within each cluster, for each selected gene, the nonparametric Kruskal-Wallis test was applied to identify genes significantly different from the median GE among all 6 groups. Significant genes with a Bonferroni's adjusted P value of less than 0.05 were included in the combined gene signature (n=2188) for the TNBC subtypes and used to predict an independent validation set as well as to classify TNBC cell lines. Each sample from the validation set was assigned to a TNBC subtype based on highest Pearson correlation and lowest P value to one of the subtypes derived from the training data set. Samples with correlations differing by a P value of less than 0.05 were considered unclassifiable.

TNBC cell-line classification. GE data for TNBC cell lines (GSE-10890 and E-TABM-157) were correlated (Spearman) to the centroids of the GE signatures for each TNBC subtype. GE data from both the TNBC tumors and cell lines were combined so that each gene was standardized to have mean=0 and SD=1. GE profiles from the cell lines were correlated to the centroids for each of the 6 TNBC subtypes. To remove size effects of the 6 gene signatures, the empirical P values were estimated for the correlations using a resampling (bootstrap, n=1000) approach and estimating correlation coefficients for each resample. Cell lines were assigned to the TNBC subtype with the highest correlation (Table 3), and those that had low correlations (<0.1) or were similar between multiple subtypes (P>0.05) were considered unclassified.

Cell proliferation/viability assays and 1050 determinations. All cell lines and culture conditions used can be found in Supplemental Methods (Table 5). Short tandem repeat (STR) DNA fingerprinting analysis was performed on all TNBC cell lines used in this study (Cell Line Genetics). All cell lines matched STR databases (ATCC, DSMZ, and Asterand), and their identity was confirmed by a certified process at Cell Line Genetics. Breast cancer cell lines and HMECs were seeded (3,000-10,000 cells) in quadruplicate wells in 96-well plates. Cells were incubated in the presence of alamar-Blue (Invitrogen), and baseline (predrug) fluorescence (Ex/Em:560/590 nm) measurements were obtained following overnight attachment. Medium was then replaced with either fresh medium (control) or medium containing half-log serial dilutions of the following drugs: 0.3-30 μM olaparib (ChemieTek), 0.3-30 μM veliparib (ChemieTek), 1-100 μM bicalutamide (IPR Pharmaceutical), 0.3-30 μM cisplatin (APP Pharmaceutical), 3-300 nM NVP-BEZ235 (Chemdea), 10-1000 nM 17-DMAG (ChemieTek), and 0.1-10 μM dasatinib (LC Laboratories). Viability was determined from measuring fluorescent intensity after metabolic reduction of alamarBlue in the presence/absence of the drug after 72 hours. Viability assays were performed in triplicate, and replicates were normalized to untreated wells. Inhibitory concentration (IC₅₀) values were determined after double-log transformation of dose response curves as previously described (Bauer J A, et al. Breast Cancer Res. 2010; 12(3):R41). For analysis of cell-line drug assays, data generated from the different cell lines representative of TNBC subtypes were compared using the nonparametric Mann-Whitney U test. All analyses and graphic representations were performed using Prism software (version 4.0c; GraphPad Software), and values are represented as the mean±SEM.

Kaplan-Meier survival analysis and Hr. Log-rank test was used to determine survival significance in TNBC subtypes from Kaplan-Meier survival curves, RFS, and DMFS. Cox proportional hazards model was used to calculate Hr, demonstrating differences in survival by pairwise comparison between TNBC subtypes (P<0.05).

Xenograft tumor studies. Five-week-old female athymic nude-Foxn1nu mice (Harlan Sprague-Dawley) were injected (s.c.) with either approximately 5×10⁶ (CAL-51, HCC1806, MDA-MB-468, and SUM185PE) or approximately 10×10⁶ (CAL-148 and SUM159PT) cells suspended in medium (200 μl) into each flank using a 22-gauge needle. The protocols describing the process of xenograft tumor formation in athymic mice were reviewed and approved by the Vanderbilt Institutional Review Board. Once tumors reached a volume of 25-50 mm³, mice were randomly allocated to treatment or vehicle arms. Treatments included bicalutamide per oral (100 mg/kg/d), cisplatin i.p. (8 mg/kg/wk), or NVP-BEZ235 per oral (50 mg/kg/d) in 1:9 N-methylpyrolidone: PEG300. Tumor diameters were serially measured at the indicated times with digital calipers, and tumor volumes were calculated as width²×length/2. Data points reflect the means and SEM for 16 tumors per treatment.

Statistics. Description of the relevant statistical methods used and analyses performed are described in the relevant Methods sections above. Comparisons between cell lines representative of TNBC subtypes were performed using the nonparametric Mann-Whitney U test. Statistical significance of drug effects on tumor growth in athymic mice was determined by 2-tailed unpaired t test.

Supplemental Methods

Immunostaining. Both formalin fixed paraffin embedded (FFPE) and frozen tissue were used for immunohistochemical studies. When frozen tissue was used for immunohistochemistry, staining was performed on sections taken from the same tissue block from which RNA was isolated for microarray. AR, Ki67, EGFR and CK 5/6 expression were evaluated in frozen tissue using the DAKO (Carpinteria, Calif.) antibodies: AR (clone AR411) at a 1:50 dilution, EGFR at 1:200, CK5/6 at 1:50 and Ki67 antibody (MIB1 clone) at a 1:200 dilution for 1 h at room temperature. FFPE tissue was subject to antigen retrieval with high pH buffer (pH 8.0) followed by overnight incubation with an AR (1:30) or Ki67 (1:75) antibody dilution overnight. AR expression was scored as both the percentage of tumor cells with nuclear staining as well as the intensity of staining (scored as 0-3+). An AR intensity score was calculated as follows: (AR intensity×100)+% AR positive cells. For Ki67 the percentage of cells demonstrating nuclear staining at any intensity was recorded.

Immunoblotting. Cells were trypsinized, lysed and relative protein expression was determined by Western blot as previously described with the following antibodies; HSP90 monoclonal antibody, clone F-18 (Santa Cruz Biotechnology, Santa Cruz, Calif.) and the AR polyclonal antibody, SC-N20 (Santa Cruz Biotechnology).

Colony Formation. MFM-223, MDA-MB-453 and CAL-148 cells (3000 cells/well) were reverse-transfected with 1.25 pmole of siRNAs to AR [ONTARGET plus SMARTpool, cat #L-003400-00 (Dharmacon, Lafayette, Colo.)] or non-targeting control (ON-TARGETplus Non-targeting Pool cat #D-001810-10-05) with 0.25 μL Dharmafect #3 (MFM-223), or 0.25 μL Dharmafect #1 (MDAMB-453 and CAL-148). Colonies were stained and quantified 14 d following transfection using Cell Profiler 2.0 (Broad Institute, Cambridge, Mass.). Experiments were preformed in triplicate and error bars reflect standard deviation.

Results

Analysis of human tumor GE profiles identifies TNBC subtypes. GE profiles were obtained from 21 publicly available data sets that contained 3,247 primary human breast cancers and processed according to the flow chart in FIG. 1A. To allow for robust analysis, these data sets were further divided into training (Table 1; 14 data sets, cases n=2353) and validation data sets (Table 2; 7 data sets, cases n=894). Since the majority of these tumors lacked sufficient molecular analysis of ER, PR, and HER2, we filtered each data set for ER, PR, and HER2 mRNA expression to identify triple-negative status (see Methods for bimodal filter description; supplemental material available in Lehmann, B. D., et al., J Clin Invest, 121(7):2750-2767 (July 2011), the entire teachings of which are incorporated herein by reference). Previous studies have shown that ER and HER2 mRNA expression correlates with immunohistochemistry (IHC) and FISH analyses, respectively (Carmeci C. et al. Am J. Pathol. 1997; 150(5):1563-1570; Press M F, et al. Clin Cancer Res. 2008; 14(23):7861-7870). Using a bimodal filter on the GE data (FIG. 1B), 386 and 201 TNBC tumor samples were identified in the training and validation sets, respectively. The 386 TNBC GE profiles of the training set were robust multiarray average (RMA) normalized, summarized, transformed, and corrected for “batch effect,” resulting in 13,060 identical probes representing unique genes across all platforms. The triple-negative GE pattern is shown compared with 5 positive controls for each parameter (ER, PR, and HER2) from data sets that were confirmed IHC positive and expressed mRNA near the center of the positive bimodal peak (FIG. 1C). Of the 14 data sets in the training set, 4 (GSE-7904, E-TABM-158, MDA133, GSE-22513, GSE-28821, and GSE-28796) included IHC data for all 3 markers, while others lacked information on ER, PR, or HER2 status (Table 1). The IHC data provided were used to calculate false-positive rates for each study, defined as tumors that were predicted negative for ER, PR, or HER2 by bimodal filtering of mRNA expression, but were positive by IHC. The overall false-positive rates were 1.7%, 1.7%, and 0.9% for ER, PR, and HER2, respectively, demonstrating that bimodal filtering of data sets by mRNA expression is a reliable method for identifying TNBC tumors from data sets lacking IHC information (Table 1). The overall frequency of TNBC across the training data set was 16% and is consistent with the prevalence of TNBC previously reported in 2 other large studies performed on 3,744 cases (17%) (17) and 1,726 cases (16%) (18).

k-means and consensus clustering reveal 6 TNBC subtypes. To identify global differences in GE between TNBC subtypes, k-means clustering was performed on the most differentially expressed genes (SD>0.8). Using the silhouette width (s[i]) as a measure of relative closeness of individual samples to their clusters, k-means clustering classified 337 of the 386 TNBC tumors into 6 stable clusters (s[i]>0) and 49 tumors into 1 unstable cluster (s[i]>0) (FIG. 2A). Clustering resulted in a distribution of samples in all 7 clusters independent of each data set, n=14, indicating that confounding factors such as batch effect, RNA amplification, and sample quality did not influence cluster distribution (FIG. 8). Sample classification robustness was analyzed by consensus clustering, which involves k-means clustering by resampling (1,000 iterations) randomly selected tumor profiles. The consensus matrix is a visual representation of the proportion of times in which 2 samples are clustered together across the resampling iterations (FIG. 2B). Groups of samples that frequently cluster with one another are pictorially represented by darker shades of red. To determine the number of clusters present in the data, the area under the curve of the consensus distribution function (CDF) plot was examined (FIG. 2C). The point at which the area under the curve ceases to show marked increases with additional cluster number (k) indicates the ideal number of clusters (FIG. 2D; Monti S. Machine Learning. 2003; 52(1-2):91-118). Therefore, the optimal number of clusters is 7, as defined by the consensus plots consistent with the k-means clustering (6 stable, 1 unstable). Unsupervised dimension reduction by principal component analysis demonstrated fundamental differences in GE between tumor subtypes identified by k-means and consensus clustering (FIG. 2E).

To assess whether similar TNBC subtypes could be generated from an independent TNBC cohort, 201 TNBC samples were compiled from bimodal filtering of 7 additional publicly available data sets (Table 2). A GE signature was derived from the most differentially expressed genes found in the TNBC training set (see Methods) and used to predict which TNBC subtype was best-fit for each of the tumors in the validation set. Each sample from the validation set was assigned to 1 of the TNBC subtypes derived from the training data set based on the highest Pearson correlation and lowest P value. Samples with correlations differing by P<0.05 were considered unclassifiable. The validation set resulted in proportioned subtypes similar to those of the initial k-means clustering of the training set. After the analysis was completed, an ad hoc analysis was performed by combining the training and validation data sets (587 tumors), which resulted in 7 subtypes identified by consensus clustering (FIG. 9), with similar enrichment in gene ontologies. This further validates the stability of the subtypes and shows that increasing sample size does not change optimal cluster number. Evaluation of GE profiles of RNA obtained from laser-capture microdissection of tumor cells from 2 data sets (GSE-22513; GSE-28821; GES-28796, Table 1; GSE-5847, Table 2) showed a similar pattern of distribution across all 7 subtypes, suggesting that these subtypes are indeed representative primarily of GE resulting from epithelial tumor cells rather than stromal components surrounding the tumor (i.e., inflammatory cells, myofibroblasts, etc.) (FIG. 10).

Distinct gene ontologies are associated with each TNBC subtype. As an independent method to analyze TNBC subtypes, Gene Set Enrichment Analysis (GSE-A) (Subramanian A, et al. Proc Natl Acad Sci USA. 2005; 102(43):15545-15550) was performed on all genes from both the training and validation sets to determine the top canonical pathways associated with each TNBC subtype. The top enriched genes (P<0.05), identified from the training set used to predict the validation set, are displayed in a heat map in FIG. 3. The top canonical pathways substantially overlapped between the training and validation sets for each subtype, indicating that the subtypes were reproducibly enriched in unique pathways (Table 4). Our 7 TNBC subtypes were characterized on the basis of gene ontologies and differential GE and subsequently labeled as follows: basal-like 1 (BL1); basal-like 2 (BL2); immunomodulatory (IM); mesenchymal (M); mesenchymal stem-like (MSL); luminal androgen receptor (LAR); and unstable (UNS) (FIG. 3). Independent analysis of 5 data sets based on TNBCs identified by IHC staining (n=183) resulted in 4 clusters with GE similar to that of basal-like, IM, mesenchymal-like, and LAR subtypes (FIGS. 11A, 11B and 12).

BL1 and BL2 subtypes. The top gene ontologies for the BL1 subtype are heavily enriched in cell cycle and cell division components and pathways (cell cycle, DNA replication reactome, G₂ cell-cycle pathway, RNA polymerase, and G₁ to S cell cycle) (FIG. 3). The annotations are supported by the expression of genes associated with proliferation, such as AURKA, AURKB, CENPA, CENPF, BUB1, TTK, CCNA2, PRC1, MYC, NRAS, PLK1, and BIRC5 (FIG. 13). Elevated DNA damage response (ATR/BRCA) pathways accompany the proliferation pathways in the BL1 subtype (FIG. 3). Increased proliferation and cell-cycle checkpoint loss are consistent with the elevated expression of the DNA damage response genes observed (CHEK1, FANCA, FANCG, RAD54BP, RAD51, NBN, EXO1, MSH2, MCM10, RAD21, and MDC1) (FIG. 13).

The highly proliferative nature of this subtype is further supported by the finding of high Ki-67 mRNA expression (MKI67) (FIG. 13) and nuclear Ki-67 staining as assessed by IHC analysis (BL1+BL2=70% vs. other subtypes=42%; P<0.05) (FIGS. 14A-14B). Enrichment of proliferation genes and increased Ki-67 expression in basal-like TNBC tumors suggest that this subtype would preferentially respond to antimitotic agents such as taxanes (paclitaxel or docetaxel) (Chakravarthy A B, et al. Clin Cancer Res. 2006; 12(5):1570-1576; Bauer J A, et al. Clin Cancer Res. 2010; 16(2):681-690). This is indeed the case when comparing the percentage of patients achieving a pathologic complete response (pCR) in 42 TNBC patients treated with neoadjuvant taxane in 2 studies (Bauer J A, et al. Clin Cancer Res. 2010; 16(2):681-690; Juul N, et al. Lancet Oncol. 2010; 11(4):358-365). In these combined studies, TNBC patients whose tumors correlated to the basal-like (BL1 and BL2) subtype had a significantly higher pCR (63%; P=0.042) when treated with taxane-based therapies as compared with mesenchymal-like (31%) or LAR (14%) subtypes (FIG. 15).

The BL2 subtype displays unique gene ontologies involving growth factor signaling (EGF pathway, NGF pathway, MET pathway, Wnt/β-catenin, and IGF1R pathway) as well as glycolysis and gluconeogenesis (FIG. 3). Likewise, the BL2 subtype is uniquely enriched in growth factor receptor GE such as EGFR, MET, and EPHA2 (FIG. 13). This subtype has features suggestive of basal/myoepithelial origin as demonstrated by higher expression levels of TP63 and MME (CD10) (FIG. 13).

IM subtype. The IM subtype is enriched for gene ontologies in immune cell processes. These processes include immune cell signaling (TH1/TH2 pathway, NK cell pathway, B cell receptor [BCR] signaling pathway, DC pathway, and T cell receptor signaling), cytokine signaling (cytokine pathway, IL-12 pathway, and IL-7 pathway), antigen processing and presentation, and signaling through core immune signal transduction pathways (NFKB, TNF, and JAK/STAT signaling) (FIG. 3). The IM signaling is evidenced by immune signal transduction GE (FIG. 13), in addition to immune cell-surface antigens, cytokine signaling, complement cascade, chemokine receptors and ligands, and antigen presentation (FIG. 16). Since a similar proportion of samples that were microdissected fell into the IM subtype, it is likely that the IM characteristics are unique to the tumor cells themselves and not a reflection of immune cell infiltrate (FIG. 10). Immune signaling genes within the IM subtype substantially overlap with a gene signature for medullary breast cancer, a rare, histologically distinct form of TNBC that despite its high-grade histology is associated with a favorable prognosis (Bertucci F, et al. Cancer Res. 2006; 66(9):4636-4644).

M and MSL subtypes. The M subtype displays a variety of unique gene ontologies that are heavily enriched in components and pathways involved in cell motility (regulation of actin by Rho), ECM receptor interaction, and cell differentiation pathways (Wnt pathway, anaplastic lymphoma kinase [ALK] pathway, and TGF-β signaling) (FIG. 3). The MSL subtype shares enrichment of genes for similar biological processes with the M subtype, including cell motility (Rho pathway), cellular differentiation, and growth pathways (ALK pathway, TGF-β signaling and Wnt/β-catenin pathway). However, unique to the MSL are genes representing components and processes linked to growth factor signaling pathways that include inositol phosphate metabolism, EGFR, PDGF, calcium signaling, G-protein coupled receptor, and ERK1/2 signaling as well as ABC transporter and adipocytokine signaling (FIG. 3).

The prevalence of cell differentiation and growth factor signaling pathways is illustrated by expression of TGF-β signaling pathway components (TGFB1L1, BGN SMAD6, SMAD7, NOTCH1, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, and TGFBR3), epithelial-mesenchymal transition-associated (EMT-associated) genes (MMP2, ACTA2, SNAI2, SPARC, TAGLN, TCF4, TWIST1, ZEB1, COL3A1, COL5A2, GNG11, ZEB2, and decreased E-cadherin [CDH1] expression), growth factors (FGF, IGF, and PDGF pathways), and Wnt/β-catenin signaling (CTNNB1, DKK2, DKK3, SFRP4, TCF4, TCF7L2, FZD4, CAV1, CAV2, and CCND2) (FIG. 13). The MSL subtype is also uniquely enriched in genes involved in angiogenesis, including VEGFR2 (KDR), TEK, TIE1, and EPAS1 as well as immune signaling evidenced by an overlap in GE unique to the IM subtype (FIG. 16).

One interesting difference between the M and MSL subtypes is that the MSL subtype expresses low levels of proliferation genes (FIG. 13). This decreased proliferation is accompanied by enrichment in the expression of genes associated with stem cells (ABCA8, PROCR, ENG, ALDHA1, PER1, ABCB1, TERF21P BCL2, BMP2, and THY1), numerous HOX genes (HOXA5, HOXA10, MEIS1, MEIS2, MEOX1, MEOX2, and MSX1), and mesenchymal stem cell-specific markers (BMP2, ENG, ITGAV, KDR, NGFR, NT5E, PDGFRB, THY1, and VCAM1) (FIG. 13). The signaling pathway components differentially expressed in the M and MSL groups share similar features with a highly dedifferentiated type of breast cancer called metaplastic breast cancer, which is characterized by mesenchymal/sarcomatoid or squamous features and is chemoresistant (Gibson G R, et al. Am Surg. 2005; 71(9):725-730).

The MSL subtype also displays low expression of claudins 3, 4, and 7, consistent with a recently identified claudin-low subtype of breast cancer (FIGS. 13 and 17; Prat et al., Breast Cancer Res, 2010; 12(5):R68). Hierarchical clustering of TNBC GE profiles using the claudin-low gene predictor set (n=770) segregated a portion of the M and MSL subtypes with low claudin (3, 4, and 7), cytokeratin (KRT7, KRT8, KRT18, and KRT19), and CD24 expression (FIG. 17; Prat A, et al. Breast Cancer Res. 2010; 12(5):R68). This population of claudin-low-expressing tumors also had high expression of genes associated with EMT (FBN1, MMP2, PDGFRB, THY1, SPARC, TGFBR2, PDGFRA, TWIST, CAV1, CAV2, and SERPINE1).

LAR subtype. GE in the LAR group was the most differential among TNBC subtypes. This subtype is ER negative, but gene ontologies are heavily enriched in hormonally regulated pathways including steroid synthesis, porphyrin metabolism, and androgen/estrogen metabolism (FIG. 3). Whether other hormone-regulated pathways such as androgen receptor (AR) signaling, previously reported in ER-negative breast cancer (Hayes M J et al. Clin Cancer Res. 2008; 14(13):4038-4044), could be responsible for the GE patterns in this LAR subtype was investigated. Indeed, it was found that AR mRNA was highly expressed, on average at 9-fold greater than all other subtypes (FIG. 13). Tumors within the LAR group also expressed numerous downstream AR targets and coactivators (DHCR24, ALCAM, FASN, FKBP5, APOD, PIP, SPDEF, and CLDN8) (FIG. 13). In addition to AR mRNA expression, AR protein expression was investigated by IHC across all TNBC tumors from the Vanderbilt cohort (n=20). The percentage of tumor cells scored with nuclear AR staining and the intensity of staining were significantly higher in the LAR subtype (>10-fold; P<0.004) compared with all other TNBC subtypes (FIGS. 18A-18B). Hierarchical clustering was performed using an AR-activated gene signature (Chen C D, et al. Nat. Med. 2004; 10(0:33-39) on the training and validation TNBC tumor data sets. Hierarchical clustering with this signature segregated the majority of LAR tumor profiles from other subtypes (FIGS. 19A-19B). Tumors in the LAR subtype display luminal GE patterns, with FOXA1, KRT18, and XBP1 among the most highly expressed genes (FIG. 20A). Others have previously described a breast cancer subgroup expressing AR termed molecular apocrine (Chen C D, et al. Nat. Med. 2004; 10(1):33-39). While we do not have detailed pathology reports for all of the LAR tumors in this study, the TNBC subgroup GE centroids were used to correlate the apocrine samples from GSE-1561 (Farmer P, et al. Oncogene. 2005; 24(29):4660-4671; Table 1). The GE profiles of all 6 apocrine tumors (GSM26883, GSM26878, GSM26886, GSM26887, GSM26903, and GSM26910) described in the study strongly correlate with LAR, suggesting that the LAR TNBC subtype is composed of AR-driven tumors that include the molecular apocrine subtype.

Intrinsic molecular breast cancer subtype classification of TNBC. Breast cancers can be classified as luminal or basal-like, dependent on their expression of different cytokeratins. TNBC tumor subtypes display differential expression of both basal-like cytokeratins (KRT5, KRT6A, KRT6B, KRT14, KRT16, KRT17, KRT23, and KRT81) and luminal cytokeratins (KRT7, KRT8, KRT18, and KRT19) across the subtypes (FIGS. 20A-20B). The UNS, BL1, BL2, and M subtypes expressed higher levels of basal cytokeratin expression, while tumors within the LAR subtype lacked basal cytokeratin expression and expressed high levels of luminal cytokeratins and other luminal markers (FOXA1 and XBP1) (FIG. 20A). In addition to cytokeratin expression, breast cancers can be classified by an “intrinsic/UNC” 306-gene set into 5 major subtypes (basal-like, HER2-like, normal breast-like, luminal A, and luminal B) (Hu Z, et al. BMC Genomics. 2006; 7:96). Since TNBCs are largely considered basal-like, each of the 386 TNBC tumor profiles were correlated to the intrinsic gene set centroids of the 5 molecular subtypes, as previously described (Hu Z, et al. BMC Genomics. 2006; 7:96). Tumors were assigned to 1 of the molecular subtypes based on the highest correlation coefficient between each TNBC expression profile and the 5 molecular subtype centroids. This analysis resulted in 49% (n=188) of the TNBC training set classified as basal-like, 14% (n=54) as luminal A, 11% (n=42) as normal breast-like, 8% (n=31) as luminal B, 5% (n=19) as HER2, and 13% (n=52) as unclassifiable (FIG. 20B). This confirms that most TNBCs classify to the basal-like molecular subtype. Both the unstable tumors and BL1 tumors correlated strongly to the basal-like intrinsic molecular classification (76% and 85%, respectively). However, the BL2, 1M, and M subtypes only moderately correlated to the basal-like molecular class (31%, 58%, and 47%, respectively), with a portion of tumors unclassified (22%, 17%, and 18%, respectively) (FIG. 20B). The M and MSL subtypes displayed the largest portion of tumors classified as normal breast-like (25%, and 46%, respectively). The BL2, M, and MSL subtypes were a mixture of classifications, suggesting the intrinsic classification system may not be suitable for characterizing these TNBC subtypes. The majority of TNBC tumors within the LAR subtype were classified as either luminal A or luminal B (82%), and none were classified as basal-like, further supporting the luminal origin of the LAR subtype (FIGS. 20A-20B). While only 49% of the tumors were classified as basal-like according to the intrinsic gene set, IHC staining performed on the Vanderbilt subset of tumors (n=25) showed that the majority (88%) of TNBCs stained positive for the basal cytokeratins CK5/6. Additionally, 56% of the Vanderbilt tumors stained positive for EGFR, similar to a previous study that found 56% of n=929 pooled from 34 studies that were positive for EGFR or CK5/6 (Yang X R, et al. J Natl Cancer Inst. 2011; 103(3):250-263). There were no statistical differences between CK5/6 and EGFR staining across TNBC subtypes. Thus, the majority of TNBCs display a basal-like phenotype by IHC, while only approximately half correlate to the basal-like intrinsic gene set.

Patient relapse-free survival and distant-metastasis-free survival differs among TNBC subtypes. Relapse-free survival (RFS) between TNBC subtypes was significantly different (log-rank test; P=0.0083) (FIG. 21A), despite variability of therapy and duration of treatment. RFS was significantly decreased in the LAR subtype compared with the BL1 (hazard ratio [Hr]=2.9), IM (Hr=3.2), and MSL (Hr=10.5) subtypes (P<0.05) (FIG. 21B). RFS was significantly decreased in the M subtype compared with BL1 (Hr=2.6) and IM (Hr=2.9), while the MSL subtype had higher RFS than the M subtype (FIG. 21B). Distant-metastasis-free survival (DMFS) did not vary between TNBC subtypes (log-rank test; P=0.2176), but the M subtype had a significantly higher Hr compared with the BL1 (Hr=2.4, P<0.05) and IM (Hr=1.9, P<0.06) subtypes (FIGS. 21C and 21D). The increased RFS in the absence of increased DMFS for patients in the LAR subtype suggests that recurrence is due to local relapse. Tumor size and grade were not significantly different among TNBC subtypes, but age at diagnosis was greater in the LAR subtype (P<0.0001), potentially contributing to decreased RFS of this subtype compared with other subtypes (FIGS. 22A-22B).

TNBC cell line models for TNBC subtypes. Cell line models would facilitate preclinical experiments to define differential drug sensitivity of the distinct subtypes within this heterogeneous disease. Using the bimodal filtering approach on ER, PR, and HER2GE levels from 2 independent breast cancer cell line data sets (GSE-10890 and ETABM-157), 24 and 25 triple-negative cell lines were identified in the GSE-10890 and ETABM-157 GE data sets, respectively. Of the cell lines present in both data sets, nearly all had similar predictions of triple-negative status by bimodal filtering. Discrepancies in some cell lines (e.g., HCC1500 and HCC1937) may be the result of differences in culturing methods and/or loss of hormone receptor expression over time in culture. Analysis of these 2 data sets identified 30 nonoverlapping TNBC cell lines.

GE profiles from the cell lines were correlated to the centroids for each of the 6 TNBC subtypes. The majority of cell lines (27 of 30) were assigned to TNBC subtypes (Table 3), except for BT20, HCC1395, and SW527, which had low correlations (<0.1) or were similar between multiple subtypes (P>0.05). Of the 7 cell lines that contained known BRCA1 and BRCA2 mutations, 5 correlated with the BL1 or BL2 subtypes (HCC1937, HCC1599, HCC2157, HCC3153, and SUM149PT), consistent with this subtype containing tumors with defects in DNA repair pathways (Table 3) and gene ontologies enriched for GE involved in cell cycle and DNA repair functions (FIG. 13). Additionally, cell lines in the BL1 and BL2 subtypes were more genomically unstable, displaying significantly more chromosomal rearrangements than those in the mesenchymal subtypes (M and MSL) (average translocations, inversions, deletions=34 versus 14, respectively; P<0.01), as determined by SKY-FISH (www.path.cam.ac.uk/˜pawefish/index.html) (FIGS. 23A-23B). All cell lines that correlated to the basal-like intrinsic molecular subtype were in the BL1, BL2, or IM subtypes (Table 3). Only 2 cell lines (HCC1187 and DU4475) were placed into the 1M subtype, suggesting that the IM subtype is underrepresented in cell culture.

Cell lines in the M and MSL subtypes were generated from highly dedifferentiated tumors derived from unique pathologies (e.g., HS578T, carcinosarcoma; and SUM159PT, anaplastic carcinoma) and expressed both epithelial and mesenchymal components. All cell lines assigned to the M and MSL subtype have spindle-like morphology in 2D culture (CAL-120, CAL-51, MDA-MB-157, MDA-MB-231, MDA-MB-436, SUM159PT, HS578T, and 8T549) or stellate-like morphology in 3D (Kenny P A et al., Mol Oncol, 2007; 1:84-96). Five cell lines matched to the LAR subtype (MDA-MB-453, SUM185PE, HCC2185, CAL-148, and MFM-223).

Two distinct basal groups (A and B) have been identified by GE profiling of breast cancer cell lines (Neve R M, et al. Cancer Cell. 2006; 10(6):515-527). Basal A cell lines display epithelial characteristics and are associated with BRCA1 gene signatures, while basal B cell lines are more invasive and display mesenchymal and stem/progenitor-like characteristics. The GE analyses revealed that the majority of basal A cell lines belong to the BL1 and BL2 subtypes, while the majority of basal B cell lines fall into the M and MSL subtypes (Table 3). Hierarchical clustering analysis was tested on all TNBC cell lines using the most differentially expressed genes from the tumors to determine whether GE patterns of the cell lines are similar within TNBC subtypes (FIG. 24). Three clusters were identified: LAR, containing all 4 LAR lines; basal-like, containing lines in the BL1 and BL2 subtypes; and mesenchymal-like, containing lines in the M and MSL subtypes. This clustering analysis indicates that TNBC cell lines can be classified into 3 main groups: basal-like (BL1 and BL2); mesenchymal-like (M and MSL); and LAR. This classification will be used in subsequent sections.

TNBC cell lines have differential sensitivity to therapeutic agents. There are a variety of targeted therapies undergoing clinical investigation in patients with TNBC including those targeting PARP (Farmer H, et al. Nature. 2005; 434(7035):917-921), AR (Agoff N S et al. Am J Clin Pathol. 2003; 120(5):725-731), Src (Finn R S, et al. Breast Cancer Res Treat. 2007; 105(3):319-326), and PI3K/mTOR (Marty B, et al. Breast Cancer Res. 2008; 10(6):R101) signaling. The panel of TNBC cell lines was used to assess differential response to several agents targeting these pathways. For comparison primary human mammary epithelial cells (HMECs) were analyzed in cell viability assays. The half-maximal inhibitory concentration (IC₅₀) values were determined for the following drugs [targets]: veliparib (ABT-888) [PARP1/2]; olaparib (AZD2281) [PARP1/2]; cisplatin [DNA]; bicalutamide [AR]; 17-DMAG [Hsp90]; dasatinib [Src/Abl]; and NVP-BEZ235 [PI3K and mTOR].

Cell-cycle and DNA damage response genes are elevated in the BL1 and BL2 subtypes (FIG. 13), and 5 of the 7 lines in the cell line panel that carry BRCA1/2-mutations reside in these subtypes (Table 3). Given the previous clinical trial observations with PARP inhibitors and cisplatin (Bhattacharyya A et al. J Biol. Chem. 2000; 275(31):23899-23903; Jones P, et al. J Med. Chem. 2009; 52(22):7170-7185; Evers B, et al. Clin Cancer Res. 2008; 14(12):3916-3925), it was predicted that these agents would preferentially decrease viability in cell lines with DNA repair defects that are representative of the BL1 and BL2 subtypes. The TNBC cell line panel was treated with the PARP inhibitors veliparib and olaparib, but not all cell lines representative of the basal-like TNBC subtypes were sensitive to PARP inhibition (FIGS. 4A-4D). The BRCA1-null cell line HCC1937 was sensitive to veliparib (IC₅₀=4 μM) but not olaparib (IC₅₀>100 μM), while the BRCA1-mutant MDA-MB-436 was sensitive to both PARP inhibitors (veliparib IC₅₀=18 μM and olaparib IC₅₀=14 μM). The BRCA2-mutant cell line HCC1599 lacked sensitivity to either PARP inhibitor (veliparib IC₅₀>30 μM and olaparib IC₅₀>100 μM). Thus, in addition to BRCA1/2 status, other properties of the tumor may dictate sensitivity to a given PARP inhibitor. Unlike PARP inhibitor sensitivity, basal-like lines were significantly more sensitive to cisplatin than mesenchymal-like lines (average IC₅₀=8 μM vs. IC₅₀=16 μM, P=0.032) or LAR lines (average IC₅₀=8 μM vs. IC₅₀=15 μM, P=0.017) (FIG. 4, E and F). The BRCA1-mutant cells (SUM149PT, HCC1937, and MDA-MB-436) and BRCA2-mutant cells (HCC1599) were among the most sensitive to cisplatin treatment (FIG. 4E).

Since cell lines representative of the LAR subtype (MDA-MB-453, SUM185PE, CAL-148, and MFM-223) express high levels of AR mRNA and protein (FIG. 25A), we compared the sensitivity of TNBC cell lines to the AR antagonist bicalutamide (FIGS. 5A and 5B). IC₅₀ values for the majority of TNBC cell lines were not achieved using the highest dose of 500 μM. However, all LAR cell lines tested (SUM185PE, CAL-148, MDA-MB-453, and MFM-223) and a subset of mesenchymal-like cell lines that express low levels of AR (HS578T, 8T549, CAL-51, and MDA-MB-231) were more sensitive to bicalutamide than basal-like cell lines (average IC₅₀=227 μM vs. IC₅₀>600 μM, P=0.007; and average IC₅₀=361 μM vs. IC₅₀>600 μM, P=0.038, respectively) (FIG. 5A).

Since AR requires the Hsp90 chaperone for proper protein folding and stability (Solit D B, et al. Clin Cancer Res. 2002; 8(5):986-993), the sensitivity of the cell line panel to an Hsp90 inhibitor, 17-dimethylaminoethylamino-17-demethoxy-geldanamycin (17-DMAG), was determined. Again, the LAR cell lines were more sensitive to 17-DMAG compared with the majority of basal-like (average IC₅₀=16 nM vs. IC₅₀=81 nM; P=0.004) and mesenchymal-like (average IC₅₀=16 nM vs. IC₅₀=117 nM; P=0.05) cell lines (FIGS. 5C and 5D), albeit 17-DMAG has many other targets. These data strongly suggest that LAR tumors are driven by AR signaling and AR represents a therapeutic target for this subtype. Importantly, AR status in TNBC patients represents a molecular marker for preselection of patients for antiandrogen therapy.

To determine whether the growth of the LAR cell lines was AR dependent, MFM-223, MDA-MB-453, and SUM185PE cell lines were treated with control and AR-targeting siRNA. Knockdown of AR in the experimental samples at the protein level was verified (FIG. 25B), colony growth assays were performed, and the number of colonies formed after 14 days of siRNA transfection were analyzed. The ability of all the LAR cell lines to form colonies was significantly reduced after knockdown of AR expression as compared with control samples (MFM-223=55%, P=0.031; MDA-MB-453=51%, P=0.004; and SUM185PE=42.3%, P=0.002) (FIG. 25C), indicating that AR expression is in part responsible for tumor cell viability/survival.

GE analysis of the mesenchymal-like subtypes demonstrated enrichment in the expression of genes that make up components and pathways associated with EMT (TGFβ, ECM-receptor interaction, ALK, Wnt/β-catenin, and Rac1) and those associated with cell motility (focal adhesion, integrin signaling, Rac1, striated muscle contraction, and regulation of actin by Rho GTPase) FIG. 3). Since the nonreceptor tyrosine kinase Src plays critical roles in cell migration and the mesenchymal-like subtypes are enriched in cell motility pathways, the effect of the Src inhibitor dasatinib on the panel of TNBC lines was analyzed. Cell lines belonging to the mesenchymal-like subtypes (M and MSL) were more sensitive to dasatinib than the LAR cell lines (average IC₅₀=22 μM vs. IC₅₀=88 μM, P=0.024) (FIGS. 6A and 6B).

Since activating mutations in PIK3CA are the most frequent genetic event in breast cancer (Samuels Y, et al. Science. 2004; 304(5670):554), the TNBC cell lines were treated with the dual PI3K/mTOR inhibitor NVP-BEZ235 (Maira S M, et al. Mol Cancer Ther. 2008; 7(7):1851-1863). TNBC cell lines that have activated PI3K/AKT signaling due to PIK3CA mutations or PTEN deficiency (Table 3) were highly sensitive to NVPBEZ235 (FIG. 6C). In addition, mesenchymal-like TNBC cell lines were more sensitive to NVP-BEZ235 compared with basallike cell lines (average IC₅₀=44 nM vs. IC₅₀=201 nM; P=0.001) (FIGS. 6C and 6D), which may suggest that deregulation of the PI3K pathway is important for this subtype. LAR cell lines were also more sensitive to NVP-BEZ235 compared with basal-like cell lines (average IC₅₀=37 nM vs. 116 nM; P=0.01) (FIGS. 6C and 6D). This sensitivity can be explained by PIK3CA mutations, frequent in the LAR subtype, with all LAR cell lines containing PIK3CA-activating mutations (HCC2185, MDA-MB-453 CAL-148, MFM-223, and SUM185PE) (Table 3). While PIK3CA mutations predicted NVP-BEZ235 sensitivity, PTEN deficiencies (mutation or loss of protein expression) did not correlate with sensitivity.

Xenograft tumors derived from TNBC cell lines display differential sensitivity to therapeutic agents in vivo. In order to further analyze the susceptibility or resistance of TNBC subtypes to therapeutic agents in a more physiological setting than 2D culture, xenograft tumors were established in nude mice from cell lines representative of the basallike (HCC1806 and MDA-MB-468), mesenchymal-like (CAL-51 and SUM159PT), or LAR (SUM185PE and CAL-148) subtypes. After tumors reached an approximate volume of 25-50 mm³, the mice were treated with cisplatin, NVP-BEZ235 or bicalutamide. The sensitivity of the TNBC cell lines to the therapeutic agents when grown as 3D xenograft tumors in vivo was very similar to that seen with the cell lines grown in 2D monolayer culture. The xenograft tumors derived from the 2 cell lines representative of basal-like tumors (HCC1806 and MDA-MB-468) were highly and differentially sensitive to cisplatin and were significantly growth inhibited (P<0.0001) relative to treatment with vehicle control or the other experimental treatments (bicalutamide and NVP-BEZ235) (FIG. 7). The tumors derived from the LAR cell lines (SUM185PE and CAL-148) and the mesenchymal-like cell line that expresses low level AR protein (CAL-51) (FIGS. 25A-25C) displayed significant sensitivity to bicalutamide (FIG. 7). The xenograft tumors derived from all the cell lines carrying activating PIK3CA mutations (SUM185PE, CAL-148, CAL-51, and SUM159PT) had partial response or complete compared with NVP-BEZ235 (FIG. 7).

In summary, cell lines representative of the 6 TNBC subtypes display different sensitivities to a variety of agents, and importantly, these differences can be attributed to distinct expression of cellular components and presence of mutations in key oncogenes and tumor suppressors. The results have immediate clinical translation, as they provide a valuable platform and insights for ongoing and future clinical investigation. The data indicate that patients with basal-like TNBC should be treated with agents that engage DNA damage signaling response pathways; those with tumors expressing AR should receive bicalutamide alone or in combination with PI3K inhibitors; and those with mesenchymallike TNBC should be considered for trials exploring the activities of an Src antagonist in combination with a PI3K inhibitor.

Supplemental Results

K-means Clustering of a subset of five datasets that were identified as TNBC by IHC. Since TNBCs are not identified by GE in the clinical setting, a similar GE analysis was performed on a dataset from TNBCs identified using IHC (n=183) complied from five datasets: GSE7904 (n=22), GSE19615 (n=34), GSE20194 (n=67), E-TABM-158 (n=30) and GSE22513, GSE-XXX (n=30). This compilation included 136 tumors (74.3%) that were identified by our bimodal filtering analysis. K-means clustering performed on the most differentially expressed genes (SD>0.8) resulted in the identification of 5 TNBC subtypes (FIGS. 11A-11B). One subtype contained only three tumors and analysis of GE showed these tumors to have high levels of ER and PR FIG. 11B). These tumors were considered to be false negatives by IHC and were removed from further analysis. Comparison of these IHC-identified TNBC samples using genes differentially expressed from the six TNBC subtypes revealed similar patterns of gene enrichment (FIG. 12).

Discussion

Through GE analysis of 3247 breast cancers, demonstrate herein is that TNBCs can be reliably identified by filtering GE profiles for ER, PR, and HER2 mRNA levels. 587 TNBC GE profiles from 21 studies (training set=386 and validation set=201) were compiled. An 18% incidence rate of TNBC across the 21 independent studies (training and validation combined) was observed, similar to previously reported TNBC prevalence (Bertucci F, et al. Int J. Cancer. 2008; 123(1):236-240; Rakha E A, et al. Clin Cancer Res. 2009; 15(7):2302-2310). k-means and consensus clustering of tumor profiles revealed that TNBC is composed of 6 stable subtypes enriched in distinct gene ontologies and GE patterns. Furthermore, using a GE signature derived from TNBC patient tumors, cell-line models for each of the TNBC subtypes were identified.

Previously, the majority (50%-90%) of TNBCs have been classified as basal-like either by IHC or by correlation to the intrinsic molecular breast cancer subtypes (Bertucci F, et al. Int J. Cancer. 2008; 123(1):236-240; Rakha E A, et al. Clin Cancer Res. 2009; 15(7):2302-2310; Kreike B, et al. Breast Cancer Res. 2007; 9(5):R65). A previous TNBC study identified 5 distinct hierarchical clusters in which 91% (88 of 97) of TNBCs identified by IHC correlated to the basal-like subtype (Kreike B, et al. Breast Cancer Res. 2007; 9(5):R65). However, the study lacked molecular analysis of the tumors and conclusions were limited to clinical outcomes based on pathological markers. The relationship between TNBC and basal-like breast cancer remains controversial (Rakha E et al. Clin Cancer Res. 2008; 14(2):618). The proportion of TNBCs with basal-like GE in our study was 47%, resulting in a higher proportion of TNBCs that correlate with other molecular subtypes: luminal A (17%), normal breast-like (12%), luminal B (6%), HER2 (6%), or unclassified (12%). The study herein indicates that TNBC is not limited to tumors with a basal-like phenotype; rather it is a heterogeneous collection of tumors with distinct phenotypes, as evidenced by the diverse GE patterns and varying sensitivity of representative cell lines to the targeted therapies assessed in this study.

The BL1 and BL2 subtypes express high levels of genes involved in cell proliferation and DNA damage response, suggesting patients with basal-like tumors would benefit from agents that preferentially target highly proliferative tumors (e.g., anti-mitotic and DNA-damaging agents). Consistent with this notion, patients with basal-like tumors had up to a 4-fold higher pCR after taxane-based and radiation-based treatment as compared with patients with tumors that displayed characteristics of the ML or LAR subtypes (Bauer J A, et al. Clin Cancer Res. 2010; 16(2):681-690; Juul N, et al. Lancet Oncol. 2010; 11(4):358-365).

Nearly all of the cell lines with known mutations in BRCA1 and BRCA2 had GE patterns that correlated with the basal-like subtype, which is in agreement with the current view that BRCA-mutant tumors display a basal-like phenotype (Stefansson O A, et al. Breast Cancer Res. 2009; 11(4):R47). A number of non-BRCAmutant cell lines that correlated with the basal-like TNBC subtypes contained nearly 2-fold the number of chromosome rearrangements as all other subtypes. These findings suggest that a predominant characteristic of basal-like TNBC is genomic instability (Kwei K A et al. Mol. Oncol. 2010; 4(3):255-266). Because of GE similarities between basal-like TNBC and BRCA1-mutation carriers, PARP inhibitors are currently being tested in clinical trials for TNBC (Silver D P, et al. J Clin Oncol. 2010; 28(7):1145-1153). Despite success in BRCA-null cells, there is not sufficient evidence for PARP inhibitor efficacy in BRCA1/2-mutant breast cancer cells (Farmer H, et al. Nature. 2005; 434(7035):917-921). PARP sensitivity across a panel of TNBC cell lines did not correlate with TNBC subtype alignment or BRCA1/2-status in this study using short-term cell viability assays (72 hours). However, the synthetic lethal effects of PARP inhibition in homologous recombination-deficient cells may require multiple cell divisions and may be more appropriately tested in long-term survival assays. Other studies show that a subset of BRCA1-mutant tumors lack large-scale genomic alterations and these tumors represent a distinct disease entity and may not be susceptible to PARP inhibition (Stefansson O A, et al. Breast Cancer Res. 2009; 11(4):R47). Previous analyses of PARP inhibitors in isogenic BRCA2+/+ and BRCA2−/− cell lines suggest that sensitivity to this targeted therapy is dependent on the molecular context of the DNA repair machinery and that DNA repair requiring homologous recombination involves multiple redundant pathways (Farmer H, et al. Nature. 2005; 434(7035):917-921; Fong P C, et al. N Engl J. Med. 2009; 361(2):123-134). BRCA1 is a relatively large protein (1863 aa) that forms numerous complexes that may not be entirely disrupted when BRCA1 and BRCA2 are mutated, as opposed to BRCA-null cells. Despite an incomplete understanding of the molecular mechanism of the PARP inhibitors in vivo, these drugs have been proven to be highly effective in the clinical trial setting (41% objective response rate; 6.2 month progression-free survival) (Audeh M W, et al. J Clin Oncol. 2009; 27:5500).

It was also found that BRCA1-mutant and non-BRCA-mutant basal like cell lines had relatively higher sensitivity to cisplatin treatment compared with all other TNBC subtypes. The results are consistent with the observed 21% pCR in a clinical trial investigating neoadjuvant cisplatin as a single agent in a heterogeneous TNBC patient population (Garber J E, et al. Breast Cancer Res Treat. 2006; 105:S149; Telli M L, Ford J M. Clin Breast Cancer. 2010; 10 suppl 1:E16-E22). These data collectively suggest that the use of proliferation biomarkers such as Ki-67 and development of markers identifying defects in DNA damage response signaling could provide patient selection and tailored treatments for basal-like TNBC. Use of cisplatin as a “targeted” agent alone or in combination with antimitotics (taxanes) and/or radiation may benefit patients with this subtype and a current trial is underway with these agents (Mayer I A, et al. J Clin Oncol. 2010; 28(1):15).

The IM subtype is highly enriched in immune cell signaling. Other studies have described the presence of immune response gene signatures in ER-negative and medullary breast cancers (Bertucci F, et al. Cancer Res. 2006; 66(9):4636-4644; Teschendorff A E et al. Genome Biol. 2007; 8(8):R157). Similar to these studies, it was found elevated expression of T cell-associated genes, immune transcription factors, IFN regulatory factors, TNF, complement pathway, and antigen processing. It cannot be ruled out that the GE profile of the IM subtype comprises, at least in part, stromal components including immune cell infiltrate. However, the finding that the same proportion of microdissected tumors belongs to this group argues against stromal contamination.

The M and MSL subtypes share similar gene ontologies and GE profiles involving TGF-β, mTOR, Rac1/Rho, Wnt/β-catenin, FGFR, PDGFR, and VEGF signaling pathways. These signaling pathways are prominent in processes of EMT and stem cell-like properties of a CD44+CD24-population of normal mammary cells (Mani S A, et al. Cell. 2008; 133(4):704-715; Shipitsin M, et al. Cancer Cell. 2007; 11(3):259-273). Similarly, the MSL subtype is made up at least in part by the recently described claudin-low tumors, which lack luminal differentiation markers, high enrichment for EMT markers, immune response genes, and cancer stem cell-like features (Prat A, et al. Breast Cancer Res. 2010; 12(5):R68). Interestingly, the M and MSL subtypes differed clinically, with patients in the M subtype presenting with shorter RFS. This may be a reflection of differences in proliferation, as the M subtype displayed higher expression of proliferation-associated genes, including Ki-67. Additionally, patients with the M and MSL subtypes had decreased 5-year DMFS, consistent with enrichment in pathways associated with metastasis and motility.

Tumors within the mesenchymal-like subtypes have GE profiles that are similar to those from mesenchymal cells and metaplastic breast cancers (Hennessy B T, et al. Cancer Res. 2009; 69(10):4116-4124). Metaplastic breast cancers have lineage plasticity, including foci of spindle cell, as well as osseous or cartilaginous differentiation (Gibson G R, et al. Am Surg. 2005; 71(9):725-730). A recent study found that 47% of metaplastic breast cancers sequenced have PIK3CA mutations and have higher phosho-AKT expression (Hennessy B T, et al. Cancer Res. 2009; 69(10):4116-4124). It was found herein that TNBC mesenchymallike cell lines preferentially responded to the dual PI3K/mTOR inhibitor NVP-BEZ235. This response to NVP-BEZ235 was demonstrated in cell lines that carry PIK3CA mutations in xenografts in addition to an MSL cell line (SUM159PT) that lacks PIK3CA mutation or PTEN deficiencies, suggesting that the PI3K/mTOR pathway is important in the mesenchymal-like subtype.

The mesenchymal-like subtypes were enriched in pathways associated with EMT and cell motility. There is evidence of a prominent role for Src in tumor cells that are highly invasive, such as those that have undergone EMT (Guarino M. J Cell Physiol. 2010; 223(1):14-26). Accordingly, we found that mesenchymal-like TNBC cell lines had differential sensitivity to dasatinib. Markers of EMT may have clinical value for patient preselection for trials using dasatinib. In addition, Wnt-signaling pathways regulate EMT and may contribute to tumor cell invasion (Shin S Y, et al. Cancer Res. 2010; 70(17):6715-6724). Mutations in the Wnt/13-catenin pathway (CTNNB1, APC, and WISP3) occur frequently (52%) in metaplastic breast cancer, suggesting that deregulated Wnt/β-catenin pathway in these tumors may be a viable therapeutic target (Hayes M J et al. Clin Cancer Res. 2008; 14(13):4038-4044). Inhibitors of Wnt/fβ-catenin are of great interest and currently are in preclinical development (MacDonald B T, et al. Dev Cell. 2009; 17(1):9-26). Drugs targeting this pathway could be of value for treating mesenchymal-like TNBC.

The LAR subtype was readily subclassified by an AR gene signature and high levels of luminal cytokeratin expression. GE analysis of the LAR subtype is consistent with a prior report of a subset of ER-negative tumors expressing AR-regulated genes (Doane A S, et al. Oncogene. 2006; 25(28):3994-4008). In addition, Farmer et al. described an apocrine tumor subtype based on GE profiling that was characterized by AR expression distinguishing this tumor subtype from other basal-like tumors (Farmer P, et al. Oncogene. 2005; 24(29):4660-4671). In the GE analysis of tumors from 21 studies described herein, the prevalence of the LAR tumors was 11% (62 of 587) of TNBCs or 2% (62 of 3247) of all breast cancers. Analysis of clinical data demonstrated that patients in the LAR subtype had higher RFS but no difference in DMFS compared with all other TNBC subtypes, suggesting these patients have local relapse. The higher RFS could imply that this group of patients received ineffective therapies (standard chemotherapy); however, patients in the LAR group were significantly older at diagnosis and the extent of disease or age-associated comorbidities that affect the ability to deliver treatment as planned may have contributed to relapse. Older age at diagnosis has previously been reported in patients with AR-positive TNBC and is associated with postmenopausal status (Agoff N S et al. Am J Clin Pathol. 2003; 120(5):725-731). Whether this AR-driven subtype is arising from hormone-replacement therapy (HRT) merits further investigation; however, it is becoming clear that the risk of breast cancer increases with HRT, and synthetic progestins such as medroxyprogesterone acetate have been shown to bind and disrupt AR (Birrell S N et al. FASEB J. 2007; 21(10):2285-2293). As described herein, five (5) cell lines were identified that represent the LAR subtype and it was shown that they are sensitive to bicalutamide and 17-DMAG, suggesting that therapies targeting AR may be effective against tumors that express this hormone receptor. In fact, there is a clinical trial (NCT00468715) underway testing the effect of bicalutamide in preselected patients with ER/PR-negative AR-positive tumors. This further supports using in silico-based approaches to provide leads for trials with other targeted therapies in TNBC subtypes.

In addition to agents that target AR function, LAR cell lines were also sensitive to PI3K inhibition. This sensitivity correlated with PIK3CA mutations. All 5 LAR cells lines have activating PIK3CA mutations and are sensitive to the PI3K inhibitor NVP-BEZ235, similar to ER-positive breast cancer in which PIK3CA mutations are common (Gonzalez-Angulo A M, et al. Clin Cancer Res. 2009; 15(7):2472-2478; Stemke-Hale K, et al. Cancer Res. 2008; 68(15):6084-6091). These findings suggest simultaneous targeting of AR and the PI3K/mTOR pathway may be of clinical benefit for LAR TNBC patients, as this combination has been shown to be synergistic in AR-dependent prostate cancer cells (Liu X et al. J Clin Oncol. 2010; 28:(suppl; abstr e15049)).

The GE analysis of TNBC described herein demonstrates that with sufficient sample size, distinct subtypes of TNBC can be identified with putative molecular targets. The analyses provides biomarkers that can be used for patient selection in the design of clinical trials for TNBC as well as identification of potential markers of response to treatment. The identification of cell lines representing TNBC tumor subtypes provides key models for preclinical studies with newly developed targeted agents.

Example 2 Frequent PIKCA Mutations in AR-Positive TNBC Confer Sensitivity to PI3K and AR Inhibitors

Described herein is the further investigation of the molecular features of the LAR subtype to identify rationale combinations of drugs that would show robust efficacy against AR-positive TNBC cells with the added goal of generating preclinical data for rationale clinical trial design. It was discovered that PIK3CA kinase mutations were a frequent event in AR-positive TNBC tumors. It was found that genetic or pharmacological targeting of AR in LAR cells increased the therapeutic benefit of PI3K/mTOR inhibition. Further, it was discovered that after bicalutamide treatment of mice bearing LAR xeongraft tumors, the PI3K pathway signaling increased. Thus, the combination of AR antagonism and PI3K/mTOR inhibition was examined and an additive or synergistic effect, depending on the TNBC cell line, was found. Given that AR expression is a robust biomarker for selection of LAR TNBC patients, the preclinical findings provide the rationale for preselecting AR-positive TNBC patients for treatment with AR inhibitors and/or PI3K/mTOR inhibitors, and future clinical trials exploring the efficacy of combinations of drugs that target AR and PI3K signaling.

Results and Discussion

AR-positive TNBC tumors are enriched for PIK3CA kinase domain mutations. High frequency PIK3CA mutations in AR-positive TNBC cell lines are described in Example 1. To determine if PIK3CA mutation was the result of in vitro selection during establishment of the tumor-derived cell lines or if PIK3CA mutations were frequent in AR-positive TNBC tumors, performed Sanger sequencing was performed on 26 AR-positive TNBC cases. PCR-amplified regions from exons 9 and 20 that harbor the most frequently occurring activating mutations in PIK3CA were sequenced. Consistent with the observations in cell lines, nearly all of the detected mutations occurred at amino acid H1047 (20 of 21) with only one occurring at E545K. Mutation status was confirmed with digital droplet PCR on DNA amplified from exon 20. Using both Sanger sequencing of exons 9 and 20 and digital droplet PCR, PIK3CA mutations were significantly (P<0.0056) enriched in AR-positive TNBC tumors (17 of 26, 65.3%) versus AR-negative TNBC tumors (10 of 26, 38.4%).

Validation of PIK3CA Mutations in AR-Expressing TNBC

To verify that PIK3CA mutations were enriched in AR-expressing TNBC, RNA-seq, DNA-seq and reverse-phase protein array (RPPA) data available from The Cancer Genome Atlas (TCGA) breast cohort (Cancer Genome Atlas Network, Nature, 490:61-70 (2012)) was analyzed. Following removal of false negatives for ER, 66 TNBC samples were identified and classified according to molecular subtypes (Chen et al., Cancer informatics, 11:147-156 (2012)). The distribution of samples across the TNBC molecular subtypes was similar to that previously published (Lehmann et al., J Clin Invest, 121:2750-2767 (2011)). (BL1=14 (21.1%), BL2=6 (9.0%), IM=15 (22.7%), M=17 (25.7%), MSL=7 (10.6%) and LAR=7 (10.6%) (FIG. 26B). As expected, RNA-seq data confirmed significant levels of AR RNA (6.8 vs. 0.3, p<0.0001) and protein (1.7 vs. 0.35, p<0.0001) in the LAR subtype. Overall, PIK3CA mutations were relatively rare in TNBC cases in the TCGA dataset (4 of 66, 6.0%). However, when sorted by subtype, PIK3CA mutations were significantly enriched in LAR TNBC (3 of 7, 42.8%) compared to all other subtypes (1 of 59, 1.7%, p<0.0001), supporting our analysis of 26 TNBC cases above (FIG. 26B).

LAR TNBC Cell Lines have Increased PI3K Pathway Activation and are Sensitive to PI3K and PI3K/mTOR Inhibition.

RPPA was used to investigate AR, PTEN, active AKT (pS473 and PT308) and active GSK3β (pS21/pS9) protein levels in LAR cell lines to determine if the PI3K pathway was active in AR expressing, PI3K mutant TNBC. Activated PI3K signaling correlated with PIK3CA mutation and PTEN loss. AR-expressing TNBC cell lines expressed higher levels of active AKT as evidenced by increased pS473 (2.18 vs. −0.23, p=0.007) and pS308 (1.45 vs. −0.10, p=0.0032) and increased downstream phosphorylation of GSK3β at pS9 (1.00 vs. −0.26, p=0.0094) and pS21/pS9 (1.12 vs. −0.19, p=0.0026) (FIG. 27). Similarly, those cell lines that were null for PTEN (BT549, CAL51, HCC1395, HCC1937, HCC38, HCC70, MDA-MB-436 and MDA-MB-468) displayed higher levels of active PI3K signaling (p-AKT S473 1.28 vs. −1.28, p=0.0001, p-AKT T308 0.41 vs. −0.53, p=0.0018, p-GSK S9 0.37 vs. −0.76, p=0.0002 and pGSKαβ S9/S21 0.26 vs. −0.59, p=0.0009).

To validate the RPPA data, immunoblot analysis of the PI3K/mTOR pathway in four of the LAR cell lines, as well as primary cultures of normal mammary epithelial cells (HMEC) and the AR-dependent prostate cancer cell line LNCaP (FIG. 27), was also performed. AR receptor protein in the LAR TNBC cell lines was expressed at levels equal to or greater than LNCaP cells. AR-expressing cell lines displayed higher levels of phosphorylated AKT (S473) and phosphorylated ribosomal S6, confirming an activated PI3K pathway and downstream mTOR activation, respectively (FIG. 27).

To evaluate the clonality of AR expression, immunohistochemistry (1HC) for AR and p-AKT was performed on a cell line-based array (FIG. 27). The AR-expressing cell lines displayed differing percentage of cells positive for AR protein expression (CAL148: 20%, MDA-MB-453: 50%, MFM-223: 50% and SUM185: 90%). However, p-AKT expression was much more homogenous, indicating that activation of PI3K/AKT signaling was an earlier clonal event.

To determine the sensitivity of PIK3CA mutation-bearing LAR cell lines to PI3K inhibitors relative to other TNBC cell lines, a large panel of TNBC cell lines was treated with pan-PI3K inhibitors BKM120 (Novartis) and GDC-0941 (Genentech) or with the dual PI3K/mTOR inhibitors NVP-BEZ235 (Novartis) and GDC-0980 (Genentech). AR-expressing and other TNBC cell lines containing PIK3CA mutations were among the most sensitive to PI3K inhibition, as indicated by low half maximal inhibitory concentration (IC50) values (FIGS. 28A-28C). In contrast, PTEN deficiencies, while conferring PI3K pathway activation, did not predict for sensitivity to PI3K inhibitors (FIGS. 28A-28C). Nearly all of the PIK3CA mutant cell lines were more sensitive to PI3K/mTOR inhibitors than primary cultures of human mammary epithelial cells (HMEC).

Genetic and Pharmacologic Inhibition of AR Increases the Efficacy of PI3K Inhibition.

Whether the combined targeting of AR and PI3K would be more effective than either agent alone was investigated. To determine the effectiveness of combinatorial treatment both genetic knockdown and pharmacological inhibition of AR with shRNA and bicalutamide, respectively, in the presence and absence of PI3K inhibitors were performed (FIGS. 29A-29B). Immunoblot analysis confirmed decreased AR protein levels in three AR-expressing TNBC cell lines infected with lentiviral particles containing non-targeting shRNA or two AR-targeting hairpins (FIG. 29A). Both shRNA expression vectors targeting AR decreased cell viability across multiple doses of PI3K or PI3K/mTOR inhibitors (FIG. 29B). Efficacy of AR-targeting in combination with PI3K or PI3K/mTOR inhibitors was independent of compound, as similar results were obtained with BKM-120 and NVP-BEZ235 (FIG. 34).

Given that knockdown of AR increased the efficacy of PI3K inhibitors, pharmacological targeting of the AR was performed using bicalutamide. Both GDC-0941 and GDC-0980 displayed efficacy in AR-expressing TNBC cell lines alone and viability could be decreased further with the addition of 25 μM bicalutamide (CDX) across multiple concentrations of PI3K inhibitors (FIG. 30A). PI3K inhibition in combination with bicalutamide decreased cell viability in an additive or synergistic manner, as demonstrated by viabilities at, or below, the line of additivity. Immunoblot analysis was performed on cell lystates from untreated cells or cells treated alone or in combination with CDX, GDC-0941 and GDC-0980 to evaluate attenuation of the PI3K/mTOR pathway. Both GDC-0941 and GDC-0980 decreased activated AKT (p-S473), however, GDC-0980 was more effective at decreasing mTOR activity as measured by the decrease in levels of phosphorylated S6 (FIG. 30B). In contrast, bicalutamide (CDX) had minimal effect on either the PI3K/mTOR pathway or AR levels. Interestingly, GDC-0980 alone decreased AR levels and this decrease could be increased further by the addition of bicalutamide, suggesting that mTOR signaling contributes to the stability of AR protein, similar to crosstalk observed in prostate cancer (FIG. 30B) (Carver et al., Cancer Cell, 19:575-586 (2011)).

To determine if the decreased viability observed in AR-positive TNBC cell lines that were treated with the combination of pathway inhibitors described above was attributed to apoptotic cell death, activated caspase 3/7 levels after drug treatments were measured (FIGS. 31A-31B). Cells were treated with a high dose of adriamycin (ADR, 3□M) to measure the ability of cells to engage the apoptotic pathway. With exception of MFM-223 cells, each of the cell lines underwent robust caspase activation after 48 h of ADR treatment. While bicalutamide treatment did not induce caspase activation, treatment with both GDC-0941 and GDC-0980 alone caused caspase activation and the levels of apoptosis could be increased in combination with bicalutamide (FIG. 31A).

In addition to caspase activation, the percentage of sub 2N DNA (sub-G1)-containing cells (indicative of late stage apoptotic DNA fragmentation) was quantitated by FACs analysis. While bicalutamide treatment did not result in caspase activation, there was an increase in the sub-G1 fraction 48 h after treatment (5.25% to 18.44%) (FIG. 31B). Treatment with GDC-0941 or GDC-0980 resulted in higher sub-G1 fraction that increased in combination with bicalutamide, consistent with the caspase activation described above (FIG. 31B). Therefore, the decreased viability of AR-positive TNBC cell lines treated with a combination of AR and PI3K inhibitors can be, in part, attributed to apoptosis.

Simultaneous Targeting of AR and PI3K Decreases Viability of AR-Expressing Cell Lines Grown in a 3-D Forced Suspension Assay.

Since cell viability and drug sensitivity can be influenced by 2-D versus 3-D growth conditions, combined targeting of AR and PI3K/mTOR was evaluated in a 3-D forced suspension assay devoid of matrix. Cell lines were grown in forced suspension in agarose coated 96-well plates and treated with GDC-0941 or GDC0980 alone or in combination with bicalutamide (FIGS. 32A-32C). Increasing doses of GDC-0941 and GDC-0980 alone decreased cell aggregate size and viability in AR-expressing TNBC cell lines to a lesser degree when compared to similar treatments in 2-D (FIGS. 32A and 32B). However, the addition of bicalutamide was either additive or synergistic with PI3K/mTOR inhibition (FIG. 32B). Similar results were obtained when PI3K was inhibited with BKM120 or PI3K and mTOR were targeted with NVP-BEZ235 (FIG. 35). Together, these results indicate that simultaneous targeting of AR and PI3K/mTOR is more effective than either agent alone in AR-expressing TNBC.

PI3K is Activated after Pharmacological Inhibition of AR.

As described in Example 1, evaluation of bicalutamide in AR-expressing TNBC xenografts demonstrated significant reduction in tumor burden, however over time tumor growth occurred in the presence of drug, consistent with evolution of bicalutamide-resistant tumor cells. Since crosstalk between AR and PI3K has been demonstrated in prostate cancer, whether the level of PI3K activity changed between untreated and bicalutamide-resistant xenograft tumor cells was examined. Phospho-AKT (S473) levels were elevated in bicalutamide-resistant xenograft tumor cells (FIG. 37). Consistent with these findings were the findings herein of dose-dependent increases in p-AKT in cell lines upon genetic silencing of AR by shRNA (FIG. 38B).

Simultaneous Inhibition of AR and PI3K Signaling Decreases the Growth of LAR Cell Line-Derived Xenograft Tumors.

In order to further validate and investigate the combined targeting of AR and PI3K in AR-expressing TNBC in vivo, xenograft tumors in nude mice was established using two representative AR-positive TNBC cell lines (CAL-148 and MDA-MB-453). Following tumor establishment (25-50 mm³), mice were either treated with vehicle, bicalutamide, NVP-BEZ235, GDC-0980 alone or either NVP-BEZ235 or GDC-0980 in combination with bicalutamide. While each single agent alone significantly decreased tumor growth, both PI3K/mTOR inhibitors in combination with bicalutamide inhibited tumor growth to the greatest extent (FIG. 32C). Thus, the combined inhibition of AR and PI3K appears to be a rational treatment strategy for AR-expressing TNBC and should be considered in future clinical trial design.

Discussion

Herein we show that activating mutations in PIK3CA are a frequent event in a subset of AR-expressing TNBC (LAR) that display luminal gene expression patterns. The data herein provide the preclinical rationale for targeting AR in combination with PI3K/mTOR inhibition.

Higher levels of p-AKT in cell line xenografts after prolonged treatment with bicalutamide and increased p-AKT after siRNA knockdown of AR in cell lines is demonstrated herein. The data show that combined targeting of AR and PI3K pathway inhibition can overcome the PI3K pathway activation after AR inhibition. These studies demonstrate that both pathways cross-regulate each other by reciprocal feedback and coordinately support survival when either is repressed. The feedback between the AR and PI3K pathway may, in part, explain the enrichment of PIK3CA mutations observed in AR-positive TNBC, as this co-evolution may be necessary to overcome the increased PTEN levels driven by AR signaling.

Methods PIK3CA Mutation Evaluation.

Two independent methods were used to identify PIK3CA mutations in tumor samples. Samples were identified as mutant if they had greater than 5% of the cells positive by microdroplet PCR, as there was complete concordance with Sanger sequencing calls, or called mutant by ranger when microdroplet samples were <5% and >1% (FIGS. 33A-33B).

Sanger

To detect mutations in PIK3CA (H1047), a 588 bp fragment was PCR-amplified from exon 20 of PIK3CA using the following amplification primers; foreword: TGACATTTGAGCAAAGACCTG (SEQ ID NO: 1), reverse: CATAACATGAAATTGCGCATT (SEQ ID NO: 2). Sanger sequencing was performed on the PCR amplicon using the following internal sequencing primers; Exon Forward: ACATCATTTGCTCCAAACTGA (SEQ ID NO: 3) Reverse: CCTATGCAATCGGTCTTTGC (SEQ ID NO: 4) (Samuels et al., Science, 304:554 (2004)).

Droplet Digital PCR

The TaqMan PCR reaction mixture was assembled from a 2×ddPCR Mastermix (Bio-Rad), 20× primer, and probes (final concentrations of 900 and 250 nM, respectively) and template (variable volume) in a final volume of 20 μL. Each assembled ddPCR reaction mixture was then loaded into the sample well of an eight-channel disposable droplet generator cartridge (Bio-Rad). A volume of 70 μL of droplet generation oil (Bio-Rad) was loaded into the oil well for each channel. The cartridge was placed into the droplet generator (Bio-Rad). The cartridge was removed from the droplet generator, where the droplets that collected in the droplet well were then manually transferred with a multichannel pipet to a 96-well PCR plate. The plate was heat-sealed with a foil seal and then placed on a conventional thermal cycler and amplified to the end-point (40 cycles). Thermal cycling conditions were 95° C.×10 min (1 cycle), 94° C.×30 s and 57° C.×60 s (40 cycles), and 12° C. hold. After PCR, the 96-well PCR plate was loaded on the droplet reader (Bio-Rad), which automatically reads the droplets from each well of the plate. Analysis of the ddPCR data was performed with QuantaSoft analysis software (Bio-Rad) that accompanied the droplet reader. Primer sequences: Forward: 5′GATAAAACTGAGCAAGAGGCTTTGG′ (SEQ ID NO: 5), Reverse: 5′GCTGTTTAATTGTGTGGAAGATCCAA′ (SEQ ID NO: 6), Wild type probe: 5′-VIC-CCACCATGATGTGCA-MGB-3 (SEQ ID NO: 7), ′H1047L probe:5′-FAM-CCACCATGATGAGCA-MGB-3′ (SEQ ID NO: 8), H1047R probe: 5′-FAM-CCACCATGATGCGCA-MGB-3′ (SEQ ID NO: 9).

Subtyping TNBC Cases and Validating PIK3CA Mutations in the TCGA.

RNA-seq (lvl 3), somatic mutations (lvl2) and reverse phase protein array (RPPA, lvl3) data for breast cancer was downloaded from The Cancer Genome Atlas (tcga-data.nci.nih.gov/). RNA-seq data (RPKM) was combined and molecularly subtyped using the online TNBCtype software according to published methods (Chen et al., Cancer Informatics, 11:147-1556 (2012)). After removal of potential ER positive, 137 TNBC samples were identified and assigned a molecular subtype.

Reverse Phase Protein Array on TNBC Cell Lines.

Tumor or cell lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11×11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction. Slides were scanned on a flatbed scanner to produce 16-bit tiff image and the density was quantified by MicroVigene. Relative protein levels for each sample were determined by interpolation of each dilution curves from the standard curve (supercurve) of the slide (antibody) as previously described (Zhang et al., Bioinformatics, 25:650-654 (2009)). These values were Log2 transformed and normalized for protein loading by transformation a to linear value. Linear normalized data was then median-centered for heatmap comparisons.

Cell Proliferation/Viability Assays and IC₅₀ Determinations.

All cell lines were maintained in culture as previously described (JCI ref). Breast cancer cell lines and HMECs were seeded (3,000-10,000 cells) in quadruplicate wells in 96-well plates. Media was then replaced with either fresh media (control) or media containing half-log serial dilutions of the following drugs: GDC-0941 (10-nM-3000 nM), GDC0980 (1 nM-300 nM), BKM120 (10-nM-3000 nM) and NVP-BEZ235 (1 nM-300 nM) purchased from Selleck Chemicals (Houston, Tex.) or in combination with bicalutamide (Sigma, St. Louis, Mo.). Viability was determined from measuring fluorescent intensity after metabolic reduction of Alamar Blue in the presence/absence of drug after 72 hours. Viability assays were performed in triplicate and replicates were normalized to untreated wells. Inhibitory concentration (IC₅₀) values were determined after double-log transformation of dose response curves as previously described (Lehmann et al., J Clin Invest, 121:2750-2767 (2011)).

Quantification of Apoptosis Caspase 3/7 Activity

Cell lines were seeded in triplicate in 96-well plates. Media was removed and replaced with media containing vehicle (control) or indicated drugs. After 48 hrs, apoptosis was determined by measuring luciferase from activated caspase 3/7 upon addition of Caspase-Glo reagent (Promega, Madison, Wis.). Relative levels of caspase activity were normalized to viable cell number determined by metabolic reduction of Alamar blue.

shRNA Knockdown of AR

293FT cells were transfected with Lipofectamine 2000 (Invitrogen, Grand Island, N.Y.) the packaging vectors PAX2 and pMD2.g (Addgene, Cambridge, Mass.) along with pLKO.1-puro Misson shRNA constructs (Sigma) targeting AR or a non-targeting control. Viral media was harvested 48 h post-transfection and added to target cells along with polybrene (10 μg/mL). 72 h post-infection MDA-MB-453 (8,000 cells/well), CAL-148 (5,000 cells/well) and MFM-223 (7,000 cells/well) seeded in quadruplicate in 96-well plates. Following overnight attachment media was replaced with fresh media (control) or media containing half-log dilutions of drugs. Following incubation in drug for 72 h viability was measured with alamarBlue as previously described (Lehmann et al., J Clin Invest, 121:2750-2767 (2011)).

Forced Suspension Viability Assay

CAL-148, MFM-223 and MDA-MB-453 cells were plated (10,000 cells/well) in quadruplicate into 96-well plates coated with 0.9% agarose diluted in corresponding media. Following 5 d of growth, cells were then treated with increasing half-log concentrations of GDC-0941 (10-3000 nM), GDC0980 (1 nM-300 nM), BKM120 (10 nM-3000 nM) and NVP-BEZ235 (1 nM-300 nM) alone or in combination with 25 μM bicalutamide (CDX) for an additional 72 h, upon which cells were imaged and viability determined by Alamar blue.

Immunostaining

Formalin fixed paraffin embedded (FFPE) tissue were used for immunohistochemical studies. Androgen receptor (AR) expression and p-AKT expression were evaluated in FFPE tissue using the DAKO (Carpinteria, Calif.) antibody: AR (clone AR411) at a 1:50 dilution and AKT p473 (Cell signaling, CA) at a 1:200 dilution for 1 h at room temperature. FFPE tissue was subject to antigen retrieval with high pH buffer (pH 8.0) followed by overnight incubation with an AR (1:30) or Ki67 (1:75) antibody dilution overnight.

Immunoblotting

Cells were trypsinized, lysed and relative protein expression was determined by Western blot as previously described (JCI reference) with the following antibodies; the AR polyclonal antibody, SC-N20 (Santa Cruz Biotechnology), pS6-Ser235/236 (Cell Signaling #4856), S6 (Cell Signaling #2317), pAKT-S473 (Cell Signaling #9271), AKT (Cell Signaling #9272), PARP (Cell Signaling #9542) and GAPDH (Millipore).

Xenograft Tumor Studies.

Five-week-old female athymic nude-Foxn1nu mice (Harlan Sprague-Dawley) were injected (s.c.) with either ˜4×10⁶ (CAL-148) or ˜10×10⁶ (MDA-MB-453) cells suspended in media (200 μL) into each flank using a 22-gauge needle. Once tumors reached a volume of 25-50 mm³, mice were randomly allocated to treatment or vehicle arms. Treatments included bicalutamide p.o. (100 mg/kg/d), GDC0980 p.o. (7.5 mg/kg/d) in 5% DMSO, 0.5% carboxymethyl cellulose (MCT) or NVP-BEZ235 p.o. (50 mg/kg/d) in 0.5% MCT or the combination of bicalutamide and either GDC-0980 or NVP-BEZ235 according to the above concentrations. Tumor diameters were serially measured at the indicated times with digital calipers and tumor volumes were calculated as width²×length/2.

Supplemental Results Validation of Digital Droplet PIK3CA Mutant PCR Primers

Primers were validated using on cell lines with known PIK3CA status cells. The percentage of DNA reflected the frequency of mutant PIK3CA alleles similar to expected genotype status; HMECwt/wt=0.01%, MDA-MB-453 wt/mut=61.19% and SUM-185mut/mut=97.09% (FIG. 26A). The slightly higher mutant frequency in the heterozygous mutant cell line MDA-MB-453 is likely caused by chromosomal aneuploidy. Digital droplet PCR was far more quantitative than Sanger sequencing and both methods were 100% concordant when mutant DNA was present at levels greater than 5% (FIGS. 33A-33B).

Example 3

Cell proliferation/viability assays and IC₅₀ determinations. All cell lines were maintained in culture as previously described herein. Breast cancer cell lines and HMECs were seeded (3,000-10,000 cells) in quadruplicate wells in 96-well plates. Media was then replaced with either fresh media (control) or media containing half-log serial dilutions of the following drugs: Sorafenib, OSi-906, BMS-754807 and PF2341066 purchased from Selleck Chemicals (Houston, Tex.) Viability was determined from measuring fluorescent intensity after metabolic reduction of Alamar Blue in the presence/absence of drug after 72 hours. Viability assays were performed in triplicate and replicates were normalized to untreated wells. Inhibitory concentration (IC₅₀) values were determined after double-log transformation of dose response curves.

PDGFR inhibition selectively inhibits viability of mesenchymal-like TNBC cell lines. Bar graph displays the half-maximal inhibitory concentration (nM) of the PDGFR inhibitor sorafenib for a panel of TNBC cell lines. Colorbar below designates the TNBC subtype (basal-like=black, mesenchymal-like=grey) or normal cells (white).

IGF1R inhibition selectively inhibits viability of mesenchymal-like TNBC cell lines. Bar graph displays the half-maximal inhibitory concentration (nM) of the IGF1R inhibitor OSI-906 for a panel of TNBC cell lines. Colorbar below designates the TNBC subtype (basal-like=black, mesenchymal-like=grey) or normal cells (white).

IGF1R inhibition selectively inhibits viability of mesenchymal-like TNBC cell lines. Bar graph displays the half-maximal inhibitory concentration (nM) of the IGF1R inhibitor BMS-754807 for a panel of TNBC cell lines. Colorbar below designates the TNBC subtype (basal-like=black, mesenchymal-like=grey) or normal cells (white).

MET inhibition selectively inhibits viability of mesenchymal-like TNBC cell lines. Bar graph displays the half-maximal inhibitory concentration (nM) of the MET inhibitor PF2341066 for a panel of TNBC cell lines. Colorbar below designates the TNBC subtype (basal-like=black, mesenchymal-like=grey) or normal cells (white).

TABLE 1 Breast cancer GE data sets used to derive the TNBC training set False Positive (%) Data Set Country Case Definition BC cases IHC N (% TN) ER PR HER Refs. GSE-494^(A) Sweden Breast cancers from patients treated in Uppsala County, Sweden, 251 ER, PR 25 (10) 3.6 2.8 Miller LD, et al. An expression signature between 1987 and 1989 for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci USA. 2005; 102(38): 13550-13555. GSE-904^(A) USA Frozen tissue samples from primary, 43 ER, PR, 17 (40) 0.0 0.0 0.0 Richardson AL, et al. X sporadic and 4 BRCA1-mutant breast obtained HER2 chromosomal abnormalities in through the Harvard Breast SPORE basal-like human breast cancer. Cancer Cell. 2006; 9(2): 121-132. GSE-2109^(A,B) USA The international genomics consortium 351 Variable⁰ 60 (17) collection of breast cancer tissue samples processed by the exp0 biospecimen repository,^(g) obtained from community hospitals GSE-7390^(A,D) Europe Lymph node-negative breast cancer patients, 198 ER 29 (15) 2.5 Desmedt C, et al. Strong time systemically untreated, performed at the Bordet dependence of the 76-gene institute and part of the TRANSBIG consortium prognostic signature for node- negative breast cancer patients in the TRANSBIG multicenter independent validation series. Clin Cancer Res. 2007; 13(11): 3207-3214. E-TABM- USA Frozen tumors collected from patients that received 100 ER, PR, 30 (23) 0.8 2.3 2.3 Chin K, et al. Genomic and 158^(E) adjuvant chemotherapy (typically adriamycin and HER2 transcriptional aberrations CTX) at UC San Francisco and the California linked to breast cancer Pacific Medical Center between 1989 and 1997 Cancer Cell. 2006; 10(6): 529-541. Gse-2034^(A) Netherlands Lymph node-negative relapse-free patients 286 ER 53 (19) 3.1 Wang Y, et al. Gene-expression (80) and lymph node-negative patients that profiles to predict distant developed a distant metastasis (106) treated metastasis of lymph-node- at Erasmus Medical Center negative primary breast cancer. Lancet. 2005; 365(9460): 671-679. GSE-2990^(A) Sweden, United Invasive breast cancer from Uppsala, Sweden 189 ER 11 (6)  1.1 Sotiriou C, et al. Gene Kingdom (88), of which 64 received tamoxifen only, or from expression profiling in breast John Radcliffe, Oxford, United Kingdom (101) of cancer: understanding the which all received mixed hormone and chemotherapy molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst. 2006; 98(4): 262-272. False Positive Data Data Set Country Case Definition BC cases IHC N (% TN) (%) Refs. Set Country GSE-1456^(A) Sweden Breast cancer patients receiving surgery at Karolinska Hospital 159 NA 22 (14) Pawitan Y, et al. Gene expression profiling between 1994 and 1996 spares early breast cancer patients from adjuvant therapy: derived and validated in two population- based cohorts. Breast Cancer Res. 2005; 7(6): R953-R964. GSE-22513^(A), USA Invasive breast cancer pretreatment biopsies taken, 112 ER, PR, 25 (22) 0.0 0.0 0.0 GSE-28821, from patients at the Vanderbilt-Ingram Cancer Center HER2 GSE-28796 GSE-11121^(A) Germany Lymph node-negative breast cancer patients 200 NA 19 (10) Schmidt M, et al. The humoral treated at the Johannes Gutenberg University Mainz immune system has a key between 1988 and 1998. Patents were all treated prognostic impact in node- with surgery without adjuvant therapy negative breast cancer. Cancer Res. 2008; 68 (13): 5405-5413. GSE-2603^(A) USA Primary breast cancers surgically resected 99 ER, PR 32 (32) 0.0 0.0 Minn AJ, et al. Genes that at the Memorial Sloan-Kettering Cancer Center mediate breast cancer metastasis to lung. Nature. 2005; 436(7050): 518-524. MDA133^(F) USA Tumors from preoperative paclitaxel and 5-FU, 133 ER, PR, 21 (16) 0.0 3.0 0.8 Gibson GR, Qian D, Ku JK, Lai LL. doxorubicin, and CTX performed at the HER2 Metaplastic breast cancer: University of Texas MD Anderson Cancer Center clinical features and outcomes. Am Surg. 2005; 71 (9): 725-730. GSE-5364^(A) Singapore Tumors from the National Cancer Centre of Singapore 183 NA 31 (17) Yu K, et al. A precisely regulated gene expression cassette potently modulates metastasis and survival in multiple solid cancers. PLoS Genet. 2008; 4 (7): e1000129. GSE-1561^(A) Belgium Tumors from patients with invasive or inflammatory 49 ER, PR 16 (33) 0.0 0.0 Farmer P, et al. Identification of breast cancers treated with 5-FU, epirubicin, and molecular apocrine breast CTX obtained by the European Organization for tumours by microarray analysis. Research and Treatment, Brussels, Belgium Oncogene. 2005; 24(29): 4660-4671. TOTAL 2353 386 (16)  1.7 1.7 0.9

TABLE 2 Breast Cancer GE data sets used to derive the TNBC validation set False Data BC N Positive (%) Set Country Case Definition cases IHC (% TN) ER PR HER Refs. GSE- Netherlands Tumors from patients with lymph node-negative 58 N/A 17 Minn AJ, et al. Genes 5327^(A,B) breast cancer, who did not receive systemic (30) that mediate breast neoadjuvant or adjuvant therapy (EMC-344) at cancer metastasis to Erastimus Medical Center, Rotterdam. lung. Nature. Netherlands treated between 1980 and 1995 2005; 436(7050): 518-524. GSE- USA Primary breast cancers between 1993 and 2003 95 ER, HER2 17 8.3 0.0 Boersma BJ, et al. A 5847^(A) from patients receiving neoadjuvant (35) stromal gene signature chemotherapy collected at Baltimore hospitals associated with inflammatory breast cancer. Int J Cancer. 2008; 122(6): 1324-1332. GSE- Netherlands Lymph node-negative breast cancers from 204 N/A 46 Bos PD, et al. Genes 12276^(A) patients with metastatic disease (114) (24) that mediate breast following relapse after chemotherapy (EMC-192) cancer metastasis to the and patients (48) Without adjavant systemic brain. Nature. 2009; therapy (EMC-286) at Erasmus Medical Center, 459(7249): 1005-1009. Rotterdam, Netherlands GSE- Europe Tumors from patients with ER-negative primary 120 HER 46 2.5 Li Y, et al. 16446^(A,B) breast cancers treated with single-agent (38) Amplification of neoadjuvant epirubicin at European hospitals LAPTM4B and and coordinated at the Institut Jules Borde, YWHAZ contributes to Brussels, Belgium chemotherapy resistance and recurrence of breast cancer. Nat Med. 2010; 16(2): 214-218. GSE- USA Tumors from patients with stage II or III 24 ER, PR, 24 Li Y, et al. 18864^(A,C) TNBCs treated with cisplatin at the HER2 (100)  Amplification of Dana-Farber/Harvard Cancer LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer. Nat Med. 2010; 16(2): 214-218. GSE- USA Breast cancers from patients and treated-with 115 ER, PR, 30 0.0 0.9 3.5 Li Y, et al. 19615^(A) adjuvant chemotherapy obtained from the HER2 (26) Amplification of Harvard Breast SPORE, Boston, Massachusetts, LAPTM4B and diagnosed between 2000 and 2003 YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer. Nat Med. 2010; 16(2): 214-218. GSE- USA Pretreatment tumors obtained from stage I-III. 278 ER, PR, 27 2.6 4.3 0.0 Juul N, et al. 20194^(A) breast cancers at the University of Texas HER2 (23) Assessment of an RNA M. D. Anderson Cancer Center interference screen- derived mitotic and ceramide pathway metagene as a predictor of response to neoadjuvant paclitaxel for primary triple- negative breast cancer: a retrospective analysis of five clinical trials. Lancet Oncol. 2010; 11(4): 358-365. TOTAL 894 201  1.7 2.6 1.7 (22) ^(A)Source: GEO. ^(B)GSE-5327 and GSE-16446 data sets are derived from ER-negative tumors by IHC. ^(C)GSE-18864 data set includes only ER, PR and HER2 negative tumors by IHC.

TABLE 3 Assignment of TNBC cell lines to subtypes Subtype TNBC Cell Correlation Histol- Intrinsic Basal Subtype Line (P Value) ogy Mutations^(A) Subtype^(B) Subtype^(C) Basal-like BL1 HCC2157 0.66 (0.00) DC BRCA1; STAT4; UTX Basal Basal A HCC1599 0.62 (0.00) DC BRCA2; TP53; CTNND1; Basal Basal A TOP2B; CAMK1G HCC1937 0.28 (0.00) DC BRCA1; TP53; HER2 Basal A MAPK13; MDC1 HCC1143 0.26 (0.00) IDC TP53 Basal Basal A HCC3153 0.24 (0.00) BRCA1 Basal Basal A MDA-MB-468 0.19 (0.06) DC PTEN; RB1; SMAD4; TP53 Basal Basal A HCC38 0.19 (0.01) DC CDKN2A; TP53 Unclassified Basal B BLs SUM149PT 0.30 (0.00) INF BRCA1 Unclassified Basal B CAL-851 0.25 (0.00) IGA RB1; TP53 Basal HCC70 0.24 (0.04) DC PTEN; TP53 Basal Basal A HCC1806 0.22 (0.00) ASCC CDKN2A; TP53; UTX Unclassified Basal A HDQ-P1 0.18 (0.17) IDC TP53 Unclassified IM HCC1187 0.22 (0.00) DC TP53; CTNNA1; DDX18; Basal Basal A HUWE1; NFKBIA DU4475 0.17 (0.00) DC APC; BRAPL MAP2K4; RB1 Unclassified Mesenchymal-like M BT-549 0.21 (0.00) IDC PTEN; RB1; TP53 Unclassified Basal B CAL-51 0.17 (0.00) AC PIK3CA Unclassified CAL-120 0.09 (0.00) AC TP53 Luminal B MSL HS578T 0.29 (0.00) CS CDKN2A; HRAS; TP53 Unclassified Basal B MDA-MB-157 0.25 (0.00) MBC NF1; TP53 Unclassified Basal B SUM159PT 0.14 (0.00 ANC PIK3CA; TP53; HRAS Unclassified Basal B Mda-mb-436 0.13 (0.00) IDC BRCA1; TP53 Unclassified Basal B MDA-MB-231 0.12 (0.00) IDC BRAP; CDKN2A; KRAS; NF2; Unclassified Basal B TP53; PDGFRA LAR LAR MDA-MB-453 0.53 (0.00) AC PIK3CA; CDH1; PTEN Luminal A Luminal SUM185PE 0.39 (0.00) DC PIK3CA Luminal A Luminal HCC2185 0.34 (0.00) PIK3CA Luminal A Luminal CAL-148 0.32 (0.00) AC PIK3CA; RB1; TP53; PTEN Luminal A MFM-223 0.31 (0.00) AC PIK3CA; TP53 Luminal A/B Unclassified HCC1395 DC ATR; BRCA2; CDKN2A Basal PTEN; FGFR1; PDGFRB; TP53 BT20 IDC CDKN2A; PIK3CA; TP53 HER2 Basal A SW527 Luminal B ^(A)Source: mutations taken from COSMIC database (www.sanger.ac.uk/genetics/CGP/cosmic/). ^(B)Molecular subtype determined by correlation with UNC/intrinsic breast centroids (29). ^(C)Basal subtype obtained from Neve R M et al. (32). AC, adenocarcinoma; ANC, anaplastic carcinoma; ASCC, acantholytic squamous cell carcinoma; C, carcinoma; CS, carsinosarcoma; DC, ductal carcinoma; IDC, invasive ductal carcinoma; IGA, invasive galactophoric adenocarcinoma; INF, inflammatory ductal carcinoma; MC, metaplastic carcinoma and MBC, medullary breast cancer.

TABLE 4 Top gene ontologies for TNBC subtypes in the training and validation datasets Subtype Training Set (386) Validation Set (201) BL1 DNA REPLICATION REACTOME CELL CYCLE KEGG CELL CYCLE KEGG DNA REPLICATION REACTOME RNA POLYMERASE G2 PATHWAY CELL CYCLE METHIONINE METABOLISM GLYCOSPHINGOLIPID BIOSYNTHESIS NEO CHOLESTEROL BIOSYNTHESIS LACTOSERIES CELL CYCLE ATRBRCAPATHWAY RNA POLYMERASE UBIQUITIN MEDIATED PROTEOLYSIS ATRBRCAPATHWAY G2 PATHWAY G1 TO S CELL CYCLE REACTOME PROTEASOME CASPASE CASCADE G1 TO S CELL CYCLE REACTOME GLUTAMATE METABOLISM METHIONINE METABOLISM AMINOACYL TRNA BIOSYNTHESIS FASPATHWAY GLYCOSPHINGOLIPID BIOSYNTHESIS NEO LACTOSERIES CHOLESTEROL BIOSYNTHESIS G1 AND S PHASES PYRIMIDINE METABOLISM CYSTEINE METABOLISM AMINOACYL TRNA BIOSYNTHESIS ATMPATHWAY DNA POLYMERASE MRNA PROCESSING REACTOME CARBON FIXATION BIOSYNTHESIS OF STEROIDS ALANINE AND ASPARTATE METABOLISM KREBS TCA CYCLE PROTEASOME PYRIMIDINE METABOLISM CELLCYCLEPATHWAY PROTEASOMEPATHWAY CDMACPATHWAY SELENOAMINO ACID METABOLISM KREBS TCA CYCLE CELLCYCLEPATHWAY ALANINE AND ASPARTATE METABOLISM GAQ PATHWAY AMINOACYL TRNA BIOSYNTHESIS FASPATHWAY PROTEASOME BL2 PORPHYRIN AND CHLOROPHYLL METABOLISM BLADDER CANCER GATA3PATHWAY GATA3PATHWAY STEMPATHWAY EPITHELIAL CELL SIGNALING IN HELICOBACTER PYLORI PARKINSONS DISEASE INFECTION STARCH AND SUCROSE METABOLISM CARDIACEGFPATHWAY EGFPATHWAY NICOTINATE AND NICOTINAMIDE METABOLISM INSULINPATHWAY EDG1PATHWAY RENAL CELL CARCINOMA PANTOTHENATE AND COA BIOSYNTHESIS WNT SIGNALING TOLLPATHWAY AMINOACYL TRNA BIOSYNTHESIS RENIN ANGIOTENSIN SYSTEM GALACTOSE METABOLISM ECM RECEPTOR INTERACTION O GLYCAN BIOSYNTHESIS PHOTOSYNTHESIS ATMPATHWAY NTHIPATHWAY HUNTINGTONS DISEASE AMINOSUGARS METABOLISM IL6PATHWAY EICOSANOID SYNTHESIS G1 TO S CELL CYCLE REACTOME DORSO VENTRAL AXIS FORMATION FOCAL ADHESION NGFPATHWAY IGF1PATHWAY SPRYPATHWAY UBIQUITIN MEDIATED PROTEOLYSIS ECMPATHWAY GLIOMA METPATHWAY TPOPATHWAY CDMACPATHWAY G2PATHWAY ARFPATHWAY WNT BETA CATENIN PATHWAY P38 MAPK PATHWAY INSULIN RECEPTOR PATHWAY IN CARDIAC CHOLERA INFECTION MYOCYTES HYPERTROPHY MODEL METPATHWAY WNT BETA CATENIN PATHWAY P53 SIGNALING PATHWAY ERKPATHWAY CARDIACEGFPATHWAY FMLPPATHWAY RASPATHWAY GLYCOLYSIS NFKBPATHWAY ATMPATHWAY UCALPAINPATHWAY IGF1RPATHWAY GSK3PATHWAY GLYCOSAMINOGLYCAN DEGRADATION GLYCOLYSIS AND GLUCONEOGENESIS GALACTOSE METABOLISM EPOPATHWAY ERK1 ERK2 MAPK PATHWAY SPRYPATHWAY GLUCONEOGENESIS TRKA RECEPTOR 1 AND 2 METHYLNAPHTHALENE DEGRADATION PHOSPHOINOSITIDE 3 KINASE PATHWAY VEGFPATHWAY PROTEASOME ETSPATHWAY P38 MAPK PATHWAY PROSTAGLANDIN SYNTHESIS REGULATION PATHOGENIC ESCHERICHIA COLI INFECTION EPEC BENZOATE DEGRADATION VIA COA LIGATION CHOLERA INFECTION NFKBPATHWAY TIDPATHWAY HEPARAN SULFATE BIOSYNTHESIS ECMPATHWAY PDGFPATHWAY ARGININE AND PROLINE METABOLISM GLYCOLYSIS PROTEASOMEPATHWAY NTHIPATHWAY EPITHELIAL CELL SIGNALING IN HELICOBACTER PYLORI INFECTION NGFPATHWAY ETSPATHWAY ERK1 ERK2 MAPK PATHWAY GALACTOSE METABOLISM GAP JUNCTION ERYTHPATHWAY GLYCOLYSIS AND GLUCONEOGENESIS MYOCYTE AD PATHWAY IM CTLA4PATHWAY NO2IL12PATHWAY NO2IL12PATHWAY CTLA4PATHWAY TH1TH2PATHWAY IL12PATHWAY CSKPATHWAY TYPE I DIABETES MELLITUS NKTPATHWAY NKCELLSPATHWAY COMPPATHWAY TH1TH2PATHWAY IL7PATHWAY TNFR2PATHWAY PROTEASOME CSKPATHWAY NKCELLSPATHWAY IL7PATHWAY TYPE I DIABETES MELLITUS AMIPATHWAY AMIPATHWAY ANTIGEN PROCESSING AND PRESENTATION ANTIGEN PROCESSING AND PRESENTATION NFKBPATHWAY IL12PATHWAY TUMOR NECROSIS FACTOR PATHWAY LAIRPATHWAY PROTEASOME TNFR2PATHWAY NKTPATHWAY DCPATHWAY T CELL SIGNAL TRANSDUCTION TIDPATHWAY DEATHPATHWAY APOPTOSIS GENMAPP APOPTOSIS GENMAPP NFKBPATHWAY DCPATHWAY PROTEASOMEPATHWAY RELAPATHWAY T CELL SIGNAL TRANSDUCTION TOB1PATHWAY TUMOR NECROSIS FACTOR PATHWAY APOPTOSIS CASPASEPATHWAY APOPTOSIS KEGG APOPTOSIS T CELL RECEPTOR SIGNALING PATHWAY NATURAL KILLER CELL MEDIATED CYTOTOXICITY CYTOKINEPATHWAY TOB1PATHWAY CASPASEPATHWAY B CELL RECEPTOR SIGNALING PATHWAY TIDPATHWAY T CELL RECEPTOR SIGNALING PATHWAY IL2PATHWAY CYTOKINEPATHWAY NATURAL KILLER CELL MEDIATED CYTOTOXICITY CELL ADHESION MOLECULES CASPASE CASCADE DEATHPATHWAY LAIRPATHWAY APOPTOSIS KEGG HEMATOPOIETIC CELL LINEAGE TOLL LIKE RECEPTOR SIGNALING PATHWAY IL3PATHWAY PROTEASOME COMPPATHWAY HEMATOPOIETIC CELL LINEAGE TCRPATHWAY RELAPATHWAY B CELL RECEPTOR SIGNALING PATHWAY IL2PATHWAY STEMPATHWAY MITOCHONDRIAPATHWAY MITOCHONDRIAPATHWAY TOLLPATHWAY CELL ADHESION MOLECULES B CELL ANTIGEN RECEPTOR TOLLPATHWAY INFLAMPATHWAY STRESSPATHWAY IL2RBPATHWAY IL2RBPATHWAY IL3PATHWAY INFLAMPATHWAY STEMPATHWAY CYTOKINE CYTOKINE RECEPTOR INTERACTION BCR SIGNALING PATHWAY PIP3 SIGNALING IN B LYMPHOCYTES HIVNEFPATHWAY TOLL LIKE RECEPTOR SIGNALING PATHWAY TCRPATHWAY 41BBPATHWAY CASPASE CASCADE B CELL ANTIGEN RECEPTOR PIP3 SIGNALING IN B LYMPHOCYTES BCR SIGNALING PATHWAY NTHIPATHWAY PROTEASOME 41BBPATHWAY CERAMIDEPATHWAY CCR5PATHWAY APOPTOSIS CYTOKINE CYTOKINE RECEPTOR INTERACTION JAK STAT SIGNALING PATHWAY INTERLEUKIN 4 PATHWAY EPOPATHWAY STRESSPATHWAY NTHIPATHWAY IL1RPATHWAY CD40PATHWAYMAP APOPTOSIS CALCINEURIN NF AT SIGNALING EICOSANOID SYNTHESIS HIVNEFPATHWAY UBIQUITIN MEDIATED PROTEOLYSIS EICOSANOID SYNTHESIS CELLCYCLEPATHWAY BCRPATHWAY CALCINEURIN NF AT SIGNALING FC EPSILON RI SIGNALING PATHWAY FC EPSILON RI SIGNALING PATHWAY KERATINOCYTEPATHWAY AMINOACYL TRNA BIOSYNTHESIS AMINOACYL TRNA BIOSYNTHESIS JAK STAT SIGNALING PATHWAY CELLCYCLEPATHWAY FASPATHWAY B CELL RECEPTOR COMPLEXES PTEN PATHWAY IL6PATHWAY B CELL RECEPTOR COMPLEXES PROTEASOMEPATHWAY DNA REPLICATION REACTOME CCR5PATHWAY FOLATE BIOSYNTHESIS ATRBRCAPATHWAY ATRBRCAPATHWAY GHPATHWAY IL6PATHWAY FOLATE BIOSYNTHESIS LEUKOCYTE TRANSENDOTHELIAL MIGRATION PEPTIDE GPCRS GLEEVECPATHWAY GLEEVECPATHWAY TNFR1PATHWAY FAS PATHWAY COMPLEMENT AND COAGULATION CASCADES ABC TRANSPORTERS GENERAL BCRPATHWAY INTERLEUKIN 4 PATHWAY EPOPATHWAY IL4RECEPTOR IN B LYPHOCYTES GHPATHWAY ADIPOCYTOKINE SIGNALING PATHWAY TPOPATHWAY PROSTAGLANDIN AND LEUKOTRIENE METABOLISM AMINOACYL TRNA BIOSYNTHESIS CDMACPATHWAY PEPTIDE GPCRS TPOPATHWAY N GLYCAN BIOSYNTHESIS HSP27PATHWAY ALZHEIMERS DISEASE TNFR1PATHWAY ACUTE MYELOID LEUKEMIA INOSITOL PHOSPHATE METABOLISM GAQ PATHWAY ACUTE MYELOID LEUKEMIA CD40PATHWAYMAP LEUKOCYTE TRANSENDOTHELIAL MIGRATION METHIONINE METABOLISM IL1RPATHWAY GPCRDB CLASS B SECRETIN LIKE DENTATORUBROPALLIDOLUYSIAN ATROPHY IL4RECEPTOR IN B LYPHOCYTES OVARIAN INFERTILITY GENES CERAMIDEPATHWAY PTEN PATHWAY FCER1PATHWAY G1 TO S CELL CYCLE REACTOME PARKINSONS DISEASE CHEMICALPATHWAY CELL CYCLE KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT ATMPATHWAY NICOTINATE AND NICOTINAMIDE METABOLISM KERATINOCYTEPATHWAY HYPERTROPHY MODEL ADIPOCYTOKINE SIGNALING PATHWAY DENTATORUBROPALLIDOLUYSIAN ATROPHY FMLPPATHWAY DICTYOSTELIUM DISCOIDEUM CAMP CHEMOTAXIS PATHWAY BIOPEPTIDESPATHWAY PANCREATIC CANCER FAS SIGNALING PATHWAY RACCYCDPATHWAY AMINOSUGARS METABOLISM M CELL COMMUNICATION PTENPATHWAY HEPARAN SULFATE BIOSYNTHESIS DNA REPLICATION REACTOME ECM RECEPTOR INTERACTION RIBOSOME ALKPATHWAY TRANSLATION FACTORS UCALPAINPATHWAY RNA POLYMERASE STRIATED MUSCLE CONTRACTION DNA POLYMERASE BASAL CELL CARCINOMA BASAL TRANSCRIPTION FACTORS REGULATION OF THE ACTIN CYTOSKELETON BY IGF1MTORPATHWAY RHO GTPASES RNA TRANSCRIPTION REACTOME TGF BETA SIGNALING PATHWAY CHOLESTEROL BIOSYNTHESIS HDACPATHWAY GLYCOSYLPHOSPHATIDYLINOSITOL ANCHOR BIOSYNTHESIS HEDGEHOG SIGNALING PATHWAY ECMPATHWAY INOSITOL PHOSPHATE METABOLISM UCALPAINPATHWAY IGF1PATHWAY EIF4PATHWAY ECMPATHWAY RIBOSOMAL PROTEINS ERK5PATHWAY CELL CYCLE KEGG FOCAL ADHESION MTORPATHWAY EDG1PATHWAY REGULATION OF THE ACTIN CYTOSKELETON BY RHO CARM ERPATHWAY GTPASES INSULINPATHWAY G1 TO S CELL CYCLE REACTOME ETHER LIPID METABOLISM MRNA PROCESSING REACTOME TELPATHWAY UBIQUITIN MEDIATED PROTEOLYSIS NOTCH SIGNALING PATHWAY WNTPATHWAY WNT BETA CATENIN PATHWAY ALKPATHWAY MEF2DPATHWAY G2PATHWAY INTEGRINPATHWAY TELPATHWAY MELANOGENESIS CELL CYCLE VEGFPATHWAY ATRBRCAPATHWAY WNTPATHWAY ETSPATHWAY DORSO VENTRAL AXIS FORMATION MSL PROSTAGLANDIN SYNTHESIS REGULATION NO2IL12PATHWAY BADPATHWAY CSKPATHWAY LAIRPATHWAY LAIRPATHWAY IL7PATHWAY TOB1PATHWAY COMPPATHWAY CTLA4PATHWAY RENIN ANGIOTENSIN SYSTEM AMIPATHWAY AMIPATHWAY TH1TH2PATHWAY CSKPATHWAY RENIN ANGIOTENSIN SYSTEM ERYTHPATHWAY PAR1PATHWAY ECM RECEPTOR INTERACTION NKTPATHWAY TOB1PATHWAY IL7PATHWAY COMPLEMENT AND COAGULATION CASCADES NKCELLSPATHWAY CARDIACEGFPATHWAY DCPATHWAY HISTIDINE METABOLISM ERYTHPATHWAY GATA3PATHWAY HEMATOPOIETIC CELL LINEAGE NDKDYNAMINPATHWAY TYPE I DIABETES MELLITUS CCR5PATHWAY IL3PATHWAY FOCAL ADHESION GLYCOSAMINOGLYCAN DEGRADATION BETA ALANINE METABOLISM IL12PATHWAY INTRINSICPATHWAY IL2PATHWAY PAR1PATHWAY PROSTAGLANDIN SYNTHESIS REGULATION ALKPATHWAY EICOSANOID SYNTHESIS CALCINEURINPATHWAY COMPPATHWAY NTHIPATHWAY CCR5PATHWAY CTLA4PATHWAY GLYCAN STRUCTURES DEGRADATION BETA ALANINE METABOLISM CALCINEURINPATHWAY GCRPATHWAY COMPLEMENT AND COAGULATION CASCADES HEMATOPOIETIC CELL LINEAGE ECM RECEPTOR INTERACTION NO1PATHWAY TCRPATHWAY VIPPATHWAY TNFR2PATHWAY UCALPAINPATHWAY NO1PATHWAY EDG1PATHWAY INTRINSICPATHWAY IL3PATHWAY STATIN PATHWAY PHARMGKB IGF1PATHWAY ALKALOID BIOSYNTHESIS II TCRPATHWAY LEUKOCYTE TRANSENDOTHELIAL MIGRATION EICOSANOID SYNTHESIS HSA04514 CELL ADHESION MOLECULES NKCELLSPATHWAY INFLAMPATHWAY VALINE LEUCINE AND ISOLEUCINE DEGRADATION MEF2DPATHWAY PPARAPATHWAY IL2RBPATHWAY SPRYPATHWAY WNT BETA CATENIN PATHWAY HDACPATHWAY HSA04510 FOCAL ADHESION STATIN PATHWAY PHARMGKB NTHIPATHWAY GLYCAN STRUCTURES DEGRADATION BCRPATHWAY SMOOTH MUSCLE CONTRACTION BCR SIGNALING PATHWAY TH1TH2PATHWAY GCRPATHWAY ECMPATHWAY GLYCEROLIPID METABOLISM GPCRPATHWAY HISTIDINE METABOLISM PDGFPATHWAY GATA3PATHWAY INTEGRIN MEDIATED CELL ADHESION KEGG PEPTIDE GPCRS FATTY ACID METABOLISM PIP3 SIGNALING IN B LYMPHOCYTES NKTPATHWAY CYTOKINE CYTOKINE RECEPTOR INTERACTION CXCR4PATHWAY INOSITOL PHOSPHATE METABOLISM TOLLPATHWAY BADPATHWAY TNFR2PATHWAY MONOAMINE GPCRS LEUKOCYTE TRANSENDOTHELIAL MIGRATION NFKBPATHWAY PPAR SIGNALING PATHWAY ECM PATH WAY AMYOTROPHIC LATERAL SCLEROSIS 1 AND 2 METHYLNAPHTHALENE DEGRADATION GLYCEROLIPID METABOLISM B CELL RECEPTOR SIGNALING PATHWAY GLYCOSPHINGOLIPID METABOLISM VIPPATHWAY MTORPATHWAY CARDIACEGFPATHWAY NICOTINATE AND NICOTINAMIDE METABOLISM ALKPATHWAY PGC1APATHWAY IL4RECEPTOR IN B LYPHOCYTES METPATHWAY GHPATHWAY WNT BETA CATENIN PATHWAY NATURAL KILLER CELL MEDIATED CYTOTOXICITY TPOPATHWAY RAC1PATHWAY BUTANOATE METABOLISM EDG1PATHWAY TGF BETA SIGNALING PATHWAY BETA ALANINE METABOLISM GSK3PATHWAY UCALPAINPATHWAY GLYCOSAMINOGLYCAN DEGRADATION GPCRPATHWAY PROPANOATE METABOLISM ERK1 ERK2 MAPK PATHWAY CELL COMMUNICATION INTEGRIN MEDIATED CELL ADHESION KEGG OVARIAN INFERTILITY GENES ARACHIDONIC ACID METABOLISM VALINE LEUCINE AND ISOLEUCINE DEGRADATION ABC TRANSPORTERS GENERAL BILE ACID BIOSYNTHESIS RHOPATHWAY IL6PATHWAY JAK STAT SIGNALING PATHWAY BCR SIGNALING PATHWAY HDACPATHWAY CELL ADHESION MOLECULES BILE ACID BIOSYNTHESIS B CELL RECEPTOR SIGNALING PATHWAY TOLLPATHWAY BCRPATHWAY SPPAPATHWAY PTENPATHWAY NDKDYNAMINPATHWAY MCALPAINPATHWAY SMOOTH MUSCLE CONTRACTION 1 AND 2 METHYLNAPHTHALENE DEGRADATION CALCIUM SIGNALING PATHWAY GPCRDB CLASS B SECRETIN LIKE GLYCEROLIPID METABOLISM IL2PATHWAY ANTIGEN PROCESSING AND PRESENTATION PROPANOATE METABOLISM ADIPOCYTOKINE SIGNALING PATHWAY MELANOMA INTEGRINPATHWAY ALKALOID BIOSYNTHESIS II ETHER LIPID METABOLISM NUCLEAR RECEPTORS CK1PATHWAY TYPE I DIABETES MELLITUS NO2IL12PATHWAY RHOPATHWAY CYTOKINE CYTOKINE RECEPTOR INTERACTION BLOOD CLOTTING CASCADE INFLAMPATHWAY DICTYOSTELIUM DISCOIDEUM CAMP CHEMOTAXIS PATHWAY DIFFERENTIATION PATHWAY IN PC12 CELL LAR CHOLESTEROL BIOSYNTHESIS GLUTATHIONE METABOLISM PENTOSE AND GLUCURONATE PENTOSE AND GLUCURONATE INTERCONVERSIONS INTERCONVERSIONS GLUTATHIONE METABOLISM BIOSYNTHESIS OF STEROIDS CHOLESTEROL BIOSYNTHESIS TYROSINE METABOLISM TYROSINE METABOLISM GAMMA HEXACHLOROCYCLOHEXANE BIOSYNTHESIS OF STEROIDS DEGRADATION PORPHYRIN AND CHLOROPHYLL METABOLISM PORPHYRIN AND CHLOROPHYLL METABOLISM ANDROGEN AND ESTROGEN METABOLISM PHENYLALANINE METABOLISM GLYCOSPHINGOLIPID METABOLISM GAMMA HEXACHLOROCYCLOHEXANE TYPE III SECRETION SYSTEM DEGRADATION GAMMA HEXACHLOROCYCLOHEXANE DEGRADATION CHREBPPATHWAY FLAGELLAR ASSEMBLY GLUTATHIONE METABOLISM CITRATE CYCLE TCA CYCLE 1 AND 2 METHYLNAPHTHALENE DEGRADATION PHENYLALANINE METABOLISM GLYCOSPHINGOLIPID METABOLISM ATP SYNTHESIS PORPHYRIN AND CHLOROPHYLL METABOLISM PHOTOSYNTHESIS

EN AND ESTROGEN METABOLISM STARCH AND SUCROSE METABOLISM PHENYLALANINE METABOLISM PORPHYRIN AND CHLOROPHYLL METABOLISM CITRATE CYCLE TCA CYCLE ARGININE AND PROLINE METABOLISM TYROSINE METABOLISM GAMMA HEXACHLOROCYCLOHEXANE DEGRADATION METABOLISM OF XENOBIOTICS BY CYTOCHROME METABOLISM OF XENOBIOTICS BY CYTOCHROME P450 P450 FRUCTOSE AND MANNOSE METABOLISM EICOSANOID SYNTHESIS CARBON FIXATION VALINE LEUCINE AND ISOLEUCINE DEGRADATION GLYCAN STRUCTURES DEGRADATION GLYCAN STRUCTURES DEGRADATION CITRATE CYCLE GLYCOSYLPHOSPHATIDYLINOSITOL ANCHOR COMPPATHWAY BIOSYNTHESIS PARKINSONS DISEASE BUTANOATE METABOLISM ANDROGEN AND ESTROGEN METABOLISM ARGININE AND PROLINE METABOLISM PANTOTHENATE AND COA BIOSYNTHESIS GLUTATHIONE METABOLISM FATTY ACID METABOLISM CK1PATHWAY RENIN ANGIOTENSIN SYSTEM CITRATE CYCLE TYROSINE METABOLISM PANTOTHENATE AND COA BIOSYNTHESIS GLUTAMATE METABOLISM PROPANOATE METABOLISM ALANINE AND ASPARTATE METABOLISM FATTY ACID METABOLISM CARBON FIXATION ANDROGEN AND ESTROGEN METABOLISM EICOSANOID SYNTHESIS GLUTAMATE METABOLISM GLYCOSAMINOGLYCAN DEGRADATION N GLYCAN BIOSYNTHESIS PHENYLALANINE METABOLISM HISTIDINE METABOLISM CHREBPPATHWAY BILE ACID BIOSYNTHESIS CK1PATHWAY PROPANOATE METABOLISM MONOAMINE GPCRS HCMVPATHVVAY SPHINGOLIPID METABOLISM TRYPTOPHAN METABOLISM P53HYPOXIAPATHWAY ALANINE AND ASPARTATE METABOLISM TRYPTOPHAN METABOLISM VALINE LEUCINE AND ISOLEUCINE DEGRADATION NICOTINATE AND NICOTINAMIDE METABOLISM PPAR SIGNALING PATHWAY GLUTAMATE METABOLISM CREBPATHWAY UCALPAINPATHWAY ATP SYNTHESIS FRUCTOSE AND MANNOSE METABOLISM FLAGELLAR ASSEMBLY KREBS TCA CYCLE TYPE III SECRETION SYSTEM OXIDATIVE PHOSPHORYLATION SPRYPATHWAY HISTIDINE METABOLISM ERYTHPATHWAY GALACTOSE METABOLISM PHOTOSYNTHESIS PENTOSE PHOSPHATE PATHWAY HISTIDINE METABOLISM OXIDATIVE PHOSPHORYLATION MCALPAINPATHWAY N GLYCAN BIOSYNTHESIS FRUCTOSE AND MANNOSE METABOLISM LINOLEIC ACID METABOLISM GLYCOSAMINOGLYCAN DEGRADATION BLOOD CLOTTING CASCADE SPHINGOLIPID METABOLISM ARACHIDONIC ACID METABOLISM GLUTAMATE METABOLISM MCALPAINPATHWAY LINOLEIC ACID METABOLISM ERYTHPATHWAY GLYCEROLIPID METABOLISM ABC TRANSPORTERS GENERAL ARGININE AND PROLINE METABOLISM BUTANOATE METABOLISM SNARE INTERACTIONS IN VESICULAR TRANSPORT O GLYCAN BIOSYNTHESIS SELENOAMINO ACID METABOLISM PPAR SIGNALING PATHWAY PENTOSE PHOSPHATE PATHWAY ALANINE AND ASPARTATE METABOLISM FRUCTOSE AND MANNOSE METABOLISM VALINE LEUCINE AND ISOLEUCINE DEGRADATION NO1PATHWAY NO1PATHWAY BILE ACID BIOSYNTHESIS STARCH AND SUCROSE METABOLISM STARCH AND SUCROSE METABOLISM ARGININE AND PROLINE METABOLISM CYSTEINE METABOLISM COMPLEMENT AND COAGULATION CASCADES GATA3PATHWAY GALACTOSE METABOLISM ALANINE AND ASPARTATE METABOLISM PENTOSE PHOSPHATE PATHWAY LIMONENE AND PINENE DEGRADATION ABC TRANSPORTERS GENERAL UREA CYCLE AND METABOLISM OF AMINO GROUPS OXIDATIVE PHOSPHORYLATION N GLYCAN BIOSYNTHESIS GLYCEROLIPID METABOLISM KREBS TCA CYCLE AMINOSUGARS METABOLISM ARACHIDONIC ACID METABOLISM TRYPTOPHAN METABOLISM PENTOSE PHOSPHATE PATHWAY NAPHTHALENE AND ANTHRACENE DEGRADATION OXIDATIVE PHOSPHORYLATION UNC DNA REPLICATION REACTOME ATRBRCAPATHWAY DNA POLYMERASE CELL CYCLE KEGG CELLCYCLEPATHWAY G1 TO S CELL CYCLE REACTOME CELL CYCLE G1PATHWAY G1 AND S PHASES BASAL TRANSCRIPTION FACTORS RNA TRANSCRIPTION REACTOME AMINOACYL TRNA BIOSYNTHESIS RNA POLYMERASE PYRIMIDINE METABOLISM CARM ERPATHWAY PYRIMIDINE METABOLISM ALANINE AND ASPARTATE METABOLISM ALANINE AND ASPARTATE METABOLISM AMINOACYL TRNA BIOSYNTHESIS G2PATHWAY P53PATHWAY SELENOAMINO ACID METABOLISM GLUTAMATE METABOLISM PENTOSE PHOSPHATE PATHWAY MRNA PROCESSING REACTOME PENTOSE PHOSPHATE PATHWAY Bold- shared between training and validation set

indicates data missing or illegible when filed

TABLE 5 Cell Line Culture Conditions Site Of Tumor BRCA1 Cell Line Origin Type Mutation Source Media BT20 PB IDC ATCC EMEM 10% FBS BT549 [B ODC ATCC RPMI 10% FBS CAL120 PE AC DSMZ DMEM 10% FBS CAL148 PE AC DSMZ DMEM 20% + 2 Mm L-glutamine + 1 μg/ml EGF CAL851 PE IGA DSMZ DMEM 10% FBS + 2 Mm L-glutamine DU4475 CN DC ATCC RPMI 10% FBS HCC1143 PB IDC ATCC RPMI 10% FBS HCC1187 PB DC ATCC RPMI 10% FBS HCC1395 PB DC ATCC RPMI 10% FBS HCC1599 PB DC ATCC RPMI 10% FBS HCC1806 PB ASCC ATCC RPMI glutamax 10% FBS HCC1937 PB DC X ATCC RPMI glutamax 10% FBS HCC38 PB DC ATCC RPMI 10% FBS HCC70 PB DC ATCC RPMI 10% FBS HDQP1 PB IDC DSMZ DMEM 10% FBS HS578T PB CS ATCC DMEM 10% FBS MDAMB157 PB MC ATCC DMEM 10% FBS MDAMB231 PE IDC ATCC DMEM 10% FBS MDAM436 PE IDC X ATCC DMEM 10% FBS MDAM453 PE AC ATCC DMEM 10% FBS MDAM468 PE DC ATCC DMEM 10% FBS MFM223 PE AC DSMZ MEM (with Earle's sals) + 15% FBS + 2 mM L-glutamine + 1x insulin- transferrin-sodium s MT3 PE C DSMZ RPMI 10% FBS SUM149PT PB INF X Asterand Hams F12 5% FBS + 1 μg/ml hydrocortisone + 5 μg/ml insulin SUM159PT PB ANC Asterand Hams F12 5% FBS + 1 μg/ml hydrocortisone + 5 μg/ml insulin SUM185 PE DC Asterand Hams F12 5% FBS + 1 μg/ml hydrocortisone + 5 μg/ml insulin SW527 PE ATCC DMEM 10% FBS Tumour Type (AC, adenocarcinoma; ANC, anaplastic carcinoma; ASCC, acantholytic squamous cell carcinoma; CS, Carcinosarcoma; DC ductal carcinoma; C, carcinoma; CS, carcinosarcoma; IDC, invasive d; Isolation (PB, primary breast; PE, pleural effusion; CN cutaneous nodule)

TABLE 6A Gene Categories BL1 BL2 IM M MSL LAR ACTG2 ALOX5 ADAMDEC1 ACTA2 ABCA8 ^(L) ABCA12 ADAMDEC1 CLCA2 AIM2 ACTG2 ABCB1 AKAP12 ANP32E COL5A1 ALOX5 BCL11A ACTA2 AKR1B10 APOBEC3A CTSC ANP32E BGN ^(E) ACTG2 AKR1D1 ATR3 CXCL12 APOBEC3A CAV1 ^(F) AKAP12 ALCAM ^(G) AURKA ^(A) DHCR24 APOBEC3G CAV2 ^(F) ALDHA1 ^(L) ALDH3B2 ^(G) AURKB ^(A) EGFR ^(D) BCL2A1 CCND2 ^(F) ALOX5 ALOX15B AZGP1 EPHA2 ^(D) BIRC3 COL3A1 ^(E) AOC3 APOD ^(G) BCL11A GALNT10 BTK ^(I) COL5A1 ^(E) APOBEC3G AR ^(G) BIRC5 GBP2 BTN3A3 COL6A3 ^(E) AZGP1 BLVRB BUB1 ^(A) GPR87 C1QA COL6A3 ^(E) AZGP1 BLVRB CCL5 HTRA1 C1QB CTNNB1 ^(F) BCL2 C4B CCNA2 MET ^(D) C4B DKK2 ^(F) BGN ^(E) CADPS2 CENPA ^(A) MME CASP1 DKK3 ^(F) BMP2 ^(E) CLCA2 CENPF ^(A) PYCARD CCL19 ^(H) EN1 C4B CLDN8 CHEK1 ^(C) RSAD2 CCL3 ^(H) EPHB3 CAV1 ^(F) COL5A1 CKAP2 S100A7 CCL4 ^(H) FBN1 ^(E) CAV2 ^(F) COL6A3 COBL S100A8 CCL5 ^(H) FN1 ^(E) CCND2 ^(F) CRAT CTSS S100A9 CCL8 ^(H) FOXC1 CCR2 ^(H) CUX2 CXCL10 TNFSF10 CCR1 ^(H) FZD4 ^(F) CD2 DHCR24 ^(G) CXCL11 TP63 CCR2 ^(H) GNG11 CD37 DHRS2 CXCL13 CCR5 ^(H) GPR161 CD3D EAF2 CXCL9 CCR7 ^(H) HTRA1 CD48 FAH EN1 CD2 ^(K) IGF1 ^(E) CD52 FASN EPHB3 CD37 ^(K) IGF2 ^(E) CD69 FBN1 EXO1 ^(C) CD38 ^(K) IGFBP4 CD74 FKBP5 ^(G) FANCA ^(C) CD3D ^(K) IGFBP5 CKAP2 FMO5 FANCG ^(C) CD48 ^(K) KCNK5 COL3A1 ^(L) FOXA1 ^(G) GBP1 CD52 ^(K) LAMB1 COL5A1 ^(E) G6PD IFI44L CD69 ^(K) MFGE8 COL5A2 ^(E) CALNT10 IFIH1 CD74 ^(K) MIA COL6A3 ^(E) GALNT7 IGKC CD8A ^(K) MICALL1 CORO1A GGT1 IGKV1D-13 CKAP2 MMP2 ^(E) CSF2RB GGTLC3 IGKV4-1 CORO1A NOTCH1 ^(E) CTNNB1 ^(F) HGD ITPKB CSF2RB PDGFRA CXCL12 ^(H) HMGCS2 IVD CTSC PDGFRB CXCL13 ^(H) HSD17B11 LOC100130100 CTSS PMP22 CYTIP HTRA1 LOC339562 CXCL10 ^(H) ROPN1 DKK2 ^(F) INPP4B LOC652493 CXCL11 ^(H) S100A1 DKK3 ^(F) IQGAP2 MCM10 ^(A) CXCL13 ^(H) SCRG1 DPYD KCNMA1 MDC1 ^(C) CXCL14 ^(H) SFPR4 ^(F) ENG KMO MFGE8 CXCL9 ^(H) SMAD6 ^(E) EPAS1 KRT18 ^(G) MIA CXCR4 ^(H) SMAD7 ^(E) EV12A KYNU MICALL1 CXCR6 ^(H) SNA12 ^(E) EV12B LRRC17 MSH2 ^(C) CYBB SOX10 FBN1 ^(E) MLPH MUC5B CYTIP SPARC ^(E) FCFL2 MSX2 MYBL1 DDX60 SPOCK1 FGL2 PIP ^(G) MYC ^(B) DPYD SRPX FN1 ^(E) POU2AF1 NBN ^(C) EN1 SYNM FYB RARRES3 NRAS ^(B) EVI2A TAGLN ^(E) FZD4 ^(F) S100A7 NTN3 EVI2B TCF4 ^(F) GALNT10 S100A8 PAD12 FGL2 TCF7L2 ^(F) GALNT7 S100A9 PLK1 ^(A) FYB TGFB1 ^(E) GIMAP6 SERHL2 PMP22 GBP1 TGFB1L1 ^(E) GNG11 SIDT1 POU2AF1 GBP2 TGFB2 ^(E) GZMA SPARCL1 PRC1 ^(A) GIMAP6 TGFB3 ^(E) HCLS1 SPDEF ^(G) PSMB9 GNLY TGFBR1 ^(E) HLA-DMA SPOCK1 RAD21 ^(A) GZMA TGFBR2 ^(E) HLA-DPB1 TARP RAD51 ^(C) GZMB TGFBR3 ^(E) HLA-DRA TFAP2B RAD54BP ^(C) HCLS1 TRPS1 HLA-DRB1 TNFSF10 ROPN1 HCP5 TWIST1 ^(E) HOXA10MEIS TP53TG1 RSAD2 HERC5 VIM ^(E) HOXA5 TRGC2 RTP4 HLA-DMA WWP2 HSD17B11 TRGV9 S100A1 HLA-DPB1 ZEB1 ^(E) HTRA1 TRIM36 SCRG1 HLA-DRA ZEB2 ^(E) IGF1 ^(E) UGT2B28 SOX10 HLA-DRB1 IGF2 ^(E) XBP1 ^(G) SYNM IDO1 IGFBP4 ZBTB16 TAP1 IFI35 IGFBP5 TCF7L1 IFI44L IGKC TP53BP2 ^(C) IFIH1 IGKV1D-13 TRPS1 IFNG ^(J) IGKV4-1 TTK ^(B) IGKC IL23A UBD ^(B) IGKV1D-13 IL2RG IGKV4-1 IQGAP2 IL10RA ^(J) IRF8 IL15 ^(J) ITGAV IL15RA ^(J) ITPKB IL16 ^(J) IVD IL18 ^(J) KDR IL18R1 ^(J) KDR IL18RA ^(J) LAMB1 IL1RN ^(J) LCK IL23A ^(J) LHFP IL2RA ^(J) LOC100130100 IL2RB ^(J) LOC339562 IL2RG ^(J) LOC652493 IL2RG ^(J) LRRC17 IL4 ^(J) LTB IL6 ^(J) MEIS2 ^(L) IL7 ^(J) MEOX1 ^(L) IL7R ^(J) MEOX2 ^(L) IRF1 ^(I) MMP2 IRF7 ^(I) MSX1 ^(L) IRF8 ^(I) NGFR ITK NOTCH1 IVD NT5E JAK1 NTN3 JAK2 OGN KYNU PDGFD LAMP3 PDGFRA LCK PDGFRB LOC100130100 PER1 LOC339562 PLAC8 LOC652493 PMP22 LTB POU2AF1 LYN ^(I) PROCR ^(L) NFKB1 ^(I) PTPRC NKG7 RAC2 NTN3 ROPN1 OAS1 SAMSN1 OAS2 SELL OASL SFPR4 ^(F) PLAC8 SMAD6 ^(E) POU2AF1 SMAD7 ^(E) PSMB9 SNAI2 ^(E) PTPRC SPARC ^(E) PYCARD SPARCL1 ^(E) RAC2 ^(I) SPOCK1 RARRES3 SRGN RELB SRPX RSAD2 SYNM RTP4 TAGLN ^(E) S100A8 TCF4 ^(F) SAMSN1 TCF7L2 ^(F) SELL TEK SLAMF7 TERF2IP SNX10 TGFB1 ^(E) SRGN TGFB1L1 ^(E) STAT1 ^(I) TGFB2 ^(E) STAT4 ^(I) TGFB3 ^(E) STAT5A ^(I) TGFBR1 ^(E) TAP1 TGFBR2 ^(E) TARP TGFBR3 ^(E) TFEC THBS4 TNFAIP2 THY1 ^(L) TNFRSF17 TIE1 TNFSF10 TNFRSF17 TRAC TRAC TRGC2 TRIM22 TRGV9 TWIST1 ^(E) TRIM22 VCAM1 UBD VIM ^(E) UBE2L6 XBP1 WARS ZBTB16 ZEB1 ^(E) ZEB2 ^(E) ^(A) Cell division ^(B) Cell proliferation ^(C) DNA damage ^(D) Growth factor ^(E) ECM/TGFB ^(F) WNT ^(G) AR responsive ^(H) Chemokine ^(I) Immune signal transduction ^(J) Cytokine signaling ^(K) Surface antigen ^(L) Mesenchymal stem genes

TABLE 6B TNBC Subtype Mutations BL1 BL2 IM M MSL LAR TOP2B BRCA1 TP53 APC APC MAP3K1 ATM BRCA2 STAT4 BRAF BRAF PIK3CA ATR CDKN2A STAT1 CTNNB1 BRCA RB1 BRCA1 PTCH1 RET FGFR1 CDKN2A TP53 BRCA2 PTCH2 NFKBIA GLI1 CTNNB1 CAMK1G PTEN MAP2K4 HRAS FGFR1 CDKN2A RB1 HUWE1 KRAS HRAS CLSPN RET BRAF NOTCH1 KRAS CTNND1 TP53 NOTCH4 NF1 HDAC4 UTX PIK3CA NF2 MAPK13 PTEN PDGFRA MDC1 RB1 PDGFRB NOTCH1 TP53 PIK3CA PTEN TP53 RB1 SMAD4 SMARCAL1 STAT4 TIMELESS TP53 UTX

TABLE 6C Cell Line Source Cell Line Subtype Source Website Product No. HCC1143 BL1 ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= CRL-2321 CRL-2321&Template=cellBiology HCC1599 BL1 ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= CRL-2331 CRL-2331&Template=cellBiology HCC38 BL1 ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= CRL-2314 CRL-2314&Template=cellBiology HCC2157 BL1 ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= CRL-2340 CRL-2340&Template=cellBiology HCC1937 BL1 ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= CRL-2336 CRL-2336&Template=cellBiology HCC3153 BL1 NA NA NA MDA-MB-468 BL1 ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= HTB-132 HTB-132&Template=cellBiology CAL-851 BL2 DSMZ www.dsmz.de/catalogues/details/culture/ACC-440.html?tx_dsmzresources_pi5[returnPid]=192 ACC-440 HCC70 BL2 ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= CRL-2315 CRL-2315&Template=cellBiology HDQP1 BL2 DSMZ www.dsmz/de/catalogues/details/culture/ACC-494.html?tx_dsmzresources_pi5[returnPid]=192 ACC-494 SUM149PT BL2 Asterand www.asterand.com/Asterand/human_tissues/149PT.htm SUM-149PT HCC1806 BL2 ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= CRL-2335 CRL-2335&Template=cellBiology DU4475 IM ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= HTB-123 HTB-123&Template=cellBiology HCC1187 IM ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= CRL-2322 CRL-2322&Template=cellBiology CAL-148 LAR DSMZ www.dsmz.de/catalogues/details/culture/ACC-460.html?tx_dsmzresources_pi5[returnPid]=192 ACC-460 MFM-223 LAR DSMZ www.dsmz.de/catalogues/details/culture/ACC-422.html?tx_dsmzresources_pi5[returnPid]=192 ACC-422 SUM185PE LAR Asterand wwww.asterand.com/Asterand/human_tissues/185PE.htm SUM-185PE MDA-MB-453 LAR ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= HTB-131 HTB-131&Template=cellBiology HCC2185 LAR NA NA NA BT549 M ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= HTB-122 HTB-122&Template=cellBiology CAL-120 M DSMZ www.dsmz.de/catalogues/details/culture/ACC-459.html?tx_dsmzresources_pi5[returnPid]=192 ACC-459 CAL-51 M DSMZ www.dsmz.de/catalogues/details/culture/ACC-302.html?tx_dsmzresources_pi5[returnPid]=192 ACC-302 HS578T MSL ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= HTB-126 HTB-126&Template=cellBiology MDA-MB-157 MSL ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= HTB-24 HTB-24&Template=cellBiology MDA-MB-436 MSL ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= HTB-130 HTB-130&Template=cellBiology SUM159PT MSL Asterand wwww.asterand.com/Asterand/human_tissues/159PT.htm SUM-159PT MDA-MB-231 MSL ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= HTB-26 HTB-26&Template=cellBiology BT20 ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= HTB-19 HTB-19&Template=cellBiology HCC1395 ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= CRL-2324 CRL-2324&Template=cellBiology SW527 ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= CRL-7940 CRL-7940&Template=cellBiology MCF10A ATCC www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum= CRL-10317 CRL-10317&Template=cellBiology

The teachings of all patents, published applications and references cited herein are incorporated by reference in their entirety.

While this invention has been particularly shown and described with references to example embodiments thereof, it will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the scope of the invention encompassed by the appended claims. 

1. A method of determining a triple negative breast cancer (TNBC) subtype in an individual in need thereof comprising a) determining expression of one or more genes in one or more TNBC cells of the individual; and b) comparing the expression of the one or more genes in the TNBC cells with the expression of the one or more genes in a control, wherein increased expression of one or more cell cycle genes, cell division genes, proliferation genes, DNA damage response genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC BL1 subtype; increased expression of one or more growth factor signaling genes, glycolysis genes, gluconeogenesis genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC BL2 subtype; increased expression of one or more immune cell signaling genes, cytokine signaling genes, antigen processing and presentation genes, core immune signal transduction genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC IM subtype; increased expression of one or more cell motility genes, extracellular matrix (ECM) receptor interaction genes, cell differentiation genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC M subtype; increased expression of one or more cell motility genes, cellular differentiation genes, growth pathway genes, growth factor signaling genes, angiogenesis genes, immune signaling genes, stem cell genes, HOX genes, mesenchymal stem cell-specific marker genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC MSL subtype; and increased expression of one or more hormone regulated genes in the TNBC cells compared to the control indicates that the TNBC is a TNBC LAR subtype.
 2. The method of claim 1 wherein detection of the TNBC BL1 subtype comprises selectively detecting increased expression of a gene combination comprising AURKA, AURKB, CENPA, CENPF, BUB1, BUB1B, TTK, CCNA2, PLK1, PRC1, MYC, NRAS, PLK1, BIRC5, CHEK1, FANCA, FANCG, FOXM1, HNGA1, RAD54BP, RAD51, NEKS, NBN, EXO1, MSH2, MCM10, RAD21, SIX3, Z1C1, SOX4, SOX1 and MDC1 wherein detection of increased expression of the gene combination indicates that the TNBC is TNBC BL1 subtype.
 3. The method of claim 1 wherein determination that the TNBC is a TNBC BL1 subtype further comprises detecting increased expression of Ki-67 mRNA in the TNBC cells compared to the control.
 4. The method of claim 1 wherein determination that the TNBC is a TNBC BL1 subtype further comprises detecting one or more mutated genes.
 5. The method of claim 4 wherein the one or more mutated genes comprise mutated BRCA1, STAT4, UTX, BRCA2, TP53, CTNND1, TOP2B, CAMK1G, MAPK13, MDC1, PTEN, RB1, SMAD4, CDKN2A, ATM, ATR, CLSPN, HDAC4, NOTCH1, SMARCAL1, and TIMELESS.
 6. The method of claim 1 wherein detection of the TNBC BL2 subtype comprises selectively detecting increased expression of a gene combination comprising EGFR, MET, ELF4, MAF, NUAK1, JAG1, FOSL2, 1D1, ZIC1, SOX11, 1D3, FHL2, EPHA2, TP63 and MME wherein detection of increased expression of the gene combination indicates that the TNBC is TNBC BL2 subtype.
 7. The method of claim 1 wherein determination that the TNBC is a TNBC BL2 subtype further comprises detecting one or more mutated genes.
 8. The method of claim 7 wherein the one or more mutated genes comprise mutated BRCA1, RB1, TP53, PTEN, CDKN2A, UTX, BRAC2, PTCH1, PTCH2, and RET.
 9. The method of claim 1 wherein detection of the TNBC M subtype comprises selectively detecting increased expression of a gene combination comprising TGFB1L1, BGN, SMAD6, SMAD7, NOTCH1, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TGFBR3, MMP2, ACTA2, SNAI2, SPARC, SMAD7, PDGFRA, TAGLN, TCF4, TWIST1, ZEB1, COL3A1, JAG1, EN1, MYLK, STK38L, CDH11, ETV5, IGF1R, FGFR1, FGFR2, FGFR3, TBX3, COL5A2, GNG11, ZEB2, CTNNB1, DKK2, DKK3, SFPR4, TCF4, TCF7L2, FZD4, CAV1, CAV2, CCND1 and CCND2 wherein detection of increased expression of the gene combination indicates that the TNBC is TNBC M subtype.
 10. The method of claim 1 wherein determination that the TNBC is a TNBC M subtype further comprises detecting decreased E-cadherin (CDH1) expression compared to the control.
 11. The method of claim 1 wherein determination that the TNBC is a TNBC M subtype further comprises detecting one or more mutated genes.
 12. The method of claim 11 wherein the one or more mutated genes comprise mutated PTEN, RB1, TP53, PIK3CA, APC, BRAF, CTNNB1, FGFR1, GLI1, HRAS, KRAS, NOTCH1, and NOTCH4.
 13. The method of claim 1 wherein determination that the TNBC is a TNBC M subtype further comprises detecting chromosomal amplifications in KRAS, IGF1R or MET.
 14. The method of claim 1 wherein detection of the TNBC MSL subtype comprises selectively detecting increased expression of a gene combination comprising VEGFR2 (KDR), TEK, TIE1, EPAS1, ABCA8, PROCR, ENG, ALDHA1, PER1, ABCB1, TERF21P, BCL2, BMP2, EPAS1, STAT4, PPARG, JAK1, ID1, SMAD3, TWIST1, THY1, HOXA5, HOXA10, GL13, HHEX, ZFHX4, HMBOX1, FOS, PIK3R1, MAF, MAFB, RPS6KA2, TCF4, TGFB1L1, MEIS1, MEIS2, MEOX1, MEOX2, MSX1, ITGAV, KDR, NGFR, NT5E, PDGFRA, PDGFRB, POU2F1, and VCAM1 wherein detection of increased expression of the gene combination indicates that the TNBC is TNBC MSL subtype.
 15. The method of claim 1 wherein determination that the TNBC is a TNBC MSL subtype further comprises detecting low expression of claudins 3, 4, 7 or a combination thereof compared to the control.
 16. The method of claim 1 wherein determination that the TNBC is a MSL subtype TNBC further comprises detecting one or more mutated genes.
 17. The method of claim 16 wherein the one or more mutated genes comprise mutated CDKN2A, HRAS, TP53, NF1, PIK3CA, BRCA1, BRAF, KRAS, NF2, PDGFRA, APC, CTNNB1, FGFR1, PDGFRB.
 18. The method of claim 1 wherein detection of the TNBC IM subtype comprises selectively detecting increased expression of a gene combination comprising CCL19, CCL3, CCL4, CCL5, CCL8, CCR1, CCR2, CCR5, CCR7, CD2, CD37, CD38, CD3D, CD48, CD52, CD69, CD74, and CD8A wherein detection of increased expression of the gene combination indicates that the TNBC is TNBC IM subtype.
 19. The method of claim 1 wherein determination that the TNBC is a TNBC IM subtype further comprises detecting one or more mutated genes.
 20. The method of claim 19 wherein the one or more mutated genes comprise TP53, CTNNA1, DDX18, HUWE1, NFKBIA, APC, BRAF, MAP2K4, RB1, STAT4, STAT1, and RET.
 21. The method of claim 1 wherein detection of the TNBC LAR subtype comprises selectively detecting increased expression of a gene combination comprising AR, DHCR24, ALCAM, GATA2, GATA3, IDIH1, IDIH2, CDH11, ERBB3, CUX2, FGFR4, HOPX, FASN, FKBP5, APOD, PIP, SPDEF, CLDN8, FOXA1, KRT18, and XBP1 wherein detection of increased expression of the gene combination indicates that the TNBC is TNBC LAR subtype.
 22. The method of claim 1 wherein determination that the TNBC is a LAR subtype TNBC further comprises detecting one or more mutated genes.
 23. The method of claim 22 wherein the one or more mutated genes comprise PIK3CA, CDH1, PTEN, RB1, TP53, and MAP3K1.
 24. The method of claim 2 wherein selective expression of the gene combination is detected using PCR, microarray analysis, next generation RNA sequencing, immunofluorescence, Western blot analysis or a combination thereof.
 25. The method of claim 4 wherein the one or more mutated genes is detected using a SNaPshot assay, exome sequencing, sanger gene sequencing, resequencing array analysis, mRNA analysis/cDNA sequencing polymerase chain reaction (PCR), single-strand conformation polymorphism (sscp), heteroduplex analysis (het), allele-specific oligonucleotide (aso), restriction fragment analysis, allele-specific amplification (asa), single nucleotide primer extension, oligonucleotide ligation assay (ola), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and single strand conformation polymorphism (SSCP) or a combination thereof.
 26. The method of claim 1 wherein the individual has been diagnosed with breast cancer, the individual has not been diagnosed with breast cancer, or the individual is at risk of developing breast cancer.
 27. The method of claim 1 wherein the individual is a human.
 28. The method of claim 1 wherein the TNBC cells are epithelial cells, mesenchymal cells, immune cells or a combination thereof.
 29. The method of claim 1 wherein the control is a non-cancer cell.
 30. The method of claim 29 wherein the non-cancer cell is obtained from an individual that does not have TNBC, from non-cancerous tissue from an individual with TNBC or a combination thereof.
 31. The method of claim 1 further comprising determining a treatment protocol for the triple negative breast cancer (TNBC) patient based on the TNBC subtype.
 32. The method of claim 31 wherein the TNBC BL1 or BL2 subtype is detected in the individual and the individual is treated with one or more drugs that damages DNA.
 33. The method of claim 32 wherein the one or more drugs is an alkylating-like agent, a PARP inhibitor or a combination thereof.
 34. The method of claim 33 wherein the alkylating-like drug is cisplatin and the PARP inhibitor is veliparib, olaparib or a combination thereof.
 35. The method of claim 31 wherein the TNBC ML subtype is detected in the individual and the individual is treated with one or more drugs that inhibits Src, IGF1R, MET, PDGFR or a combination thereof.
 36. The method of claim 35 wherein the one or more drugs is disatinib, OSI-906, BMS-754807, PF2341066, sorafinib or a combination thereof.
 37. The method of claim 35 further comprising treating the individual with a P13K inhibitor, a P13K/mTOR inhibitor or a combination thereof.
 38. The method of 37 wherein the P13K inhibitor is BKM-120, GDC0941 or a combination thereof, and the P13K/mTOR inhibitor is NVP-BEZ235, GDC0980 or a combination thereof.
 39. The method of claim 31 wherein the TNBC LAR subtype is detected in the individual and the individual is treated with one or more drugs that inhibit androgen receptor (AR).
 40. The method of claim 39 wherein the one or more drugs that inhibit AR is bicalutamide, MVD3100, abiraterone or a combination thereof.
 41. The method of claim 39 further comprising treating the individual with a P13K inhibitor a P13K/mTOR inhibitor or a combination thereof.
 42. The method of claim 41 wherein the P13K inhibitor is BKM-120, GDC0941 or a combination thereof, and the P13K/mTOR inhibitor is NVP-BEZ235, GDC0980 or a combination thereof.
 43. The method of claim 39 further comprising treating the individual with an inhibitor of HSP90.
 44. The method of claim 43 wherein the inhibitor of HSP90 is DMAG.
 45. A method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) subtype comprising a) contacting a cell line that is a model for the TNBC subtype of interest with an agent to be assessed; and b) determining viability of the cell line in the presence of the agent, wherein if the viability of the cell line decreases in the presence of the agent, then the agent can be used to treat the TNBC subtype of interest.
 46. The method of claim 45 wherein the TNBC subtype of interest is a TNBC BL-1 subtype, a TNBC BL-2 subtype, a TNBC IM subtype, a TNBC M subtype, a TNBC MSL subtype or a TNBC LAR subtype.
 47. A method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) BL-1 subtype comprising a) contacting one or more TNBC BL-1 subtype cell lines with an agent to be assessed; and b) determining viability of the one or more cell lines in the presence of the agent, wherein if the viability of the one or more cell lines decreases in the presence of the agent, then the agent can be used to treat the TNBC BL-1 subtype.
 48. The method of claim 47 wherein the one or more TNBC BL-1 subtype cell lines comprises HCC2157, HCC1599, HCC1937, HCC1143, HCC3153, MDA-MB-468, and HCC38.
 49. A method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) BL-2 subtype comprising a) contacting one or more TNBC BL-2 subtype cell lines with an agent to be assessed; and b) determining viability of the one or more cell lines in the presence of the agent, wherein if the viability of the one or more cell lines decreases in the presence of the agent, then the agent can be used to treat the TNBC BL-2 subtype.
 50. The method of claim 49 wherein the one or more TNBC BL-2 subtype cell lines comprises SUM149PT, CAL-851, HCC70, HCC1806 and HDQ-P1.
 51. A method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) IM subtype comprising a) contacting one or more TNBC IM subtype cell lines with an agent to be assessed; and b) determining viability of the one or more cell lines in the presence of the agent, wherein if the viability of the one or more cell lines decreases in the presence of the agent, then the agent can be used to treat the TNBC IM subtype.
 52. The method of claim 51 wherein the one or more TNBC IM subtype cell lines comprises HCC1187 and DU4475.
 53. A method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) M subtype comprising a) contacting one or more TNBC M subtype cell lines with an agent to be assessed; and b) determining viability of the one or more cell lines in the presence of the agent, wherein if the viability of the one or more cell lines decreases in the presence of the agent, then the agent can be used to treat the TNBC M subtype.
 54. The method of claim 53 wherein the one or more TNBC M subtype cell lines comprises BT-549, CAL-51 and CAL-120.
 55. A method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) MSL subtype comprising a) contacting one or more TNBC MSL subtype cell lines with an agent to be assessed; and b) determining viability of the one or more cell lines in the presence of the agent, wherein if the viability of the one or more cell lines decreases in the presence of the agent, then the agent can be used to treat the TNBC MSL subtype.
 56. The method of claim 55 wherein the one or more TNBC MSL subtype cell lines comprises HS578T, MDA-MB-157, SUM159PT, MDA-MB-436, and MDA-MB-231.
 57. A method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) LAR subtype comprising a) contacting one or more TNBC LAR subtype cell lines with an agent to be assessed; and b) determining viability of the one or more cell lines in the presence of the agent, wherein if the viability of the one or more cell lines decreases in the presence of the agent, then the agent can be used to treat the TNBC LAR subtype.
 58. The method of claim 57 wherein the one or more TNBC LAR subtype cell lines comprises MDA-MB, SUM185PE, HCC2185, CAL-148, and MFM-223.
 59. (canceled)
 60. (canceled)
 61. (canceled)
 62. (canceled) 